ANNOTATED BY SEARCHING CDD v2.17 WITH ASTRAL SEQUENCES (corresponding references begin on line 487) #1 c.37 Ancestry = 0.000 > d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd01886 - GTP/Mg2+ binding site - putative GEF interaction site - Switch I region (i.e. effector region) ~ conformation change upon GTP binding - Switch II region ~ conformation change upon GTP binding - G1 box (i.e. P-loop or the Walker A motif) ~ signature motif of phosphate-binding loop - G2 box motif: T ~ G2 overlaps with the Switch I region - G3 box ~ overlaps the Switch II region, which includes the Walker B motif; Asp forms a water-bridged contact with Mg2+; Gly is hydrogen bonded to the gamma phosphate of GTP through the backbone amide - G4 box - G5 box > d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd01884 - GTP/Mg2+ binding site - GEF interaction site ~ EF-Tu interacts with EF-Ts, the guanine nucleotide exchange factor (GEF) - Switch I region (i.e. effector region) ~ conformation change upon GTP binding - Switch II region ~ conformation change upon GTP binding - G1 box (i.e. P-loop or the Walker A motif) ~ signature motif of phosphate-binding loop - G2 box motif: T ~ G2 overlaps with the Switch I region - G3 box ~ overlaps the Switch II region, which includes the Walker B motif; Asp forms a water-bridged contact with Mg2+; Gly is hydrogen bonded to the gamma phosphate of GTP through the backbone amide - G4 box - G5 box > d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]} - NCBI Conserved Domain ID = cd01889 - GTP/Mg2+ binding site - putative GEF interaction site - Switch I region (i.e. effector region) ~ conformation change upon GTP binding - Switch II region ~ conformation change upon GTP binding - G1 box (i.e. P-loop or the Walker A motif) ~ signature motif of phosphate-binding loop - G2 box motif: T ~ G2 overlaps with the Switch I region - G3 box ~ overlaps the Switch II region, which includes the Walker B motif; Asp forms a water-bridged contact with Mg2+; Gly is hydrogen bonded to the gamma phosphate of GTP through the backbone amide - G4 box - G5 box > d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} - NCBI Conserved Domain ID = cd01887 - GTPase domain that forms a canonical Ras-like fold. It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction - GTP/Mg2+ binding site - putative GEF interaction site - Switch I region (i.e. effector region) ~ conformation change upon GTP binding - Switch II region ~ conformation change upon GTP binding - G1 box (i.e. P-loop or the Walker A motif) ~ signature motif of phosphate-binding loop - G2 box motif: T ~ G2 overlaps with the Switch I region - G3 box ~ overlaps the Switch II region, which includes the Walker B motif; Asp forms a water-bridged contact with Mg2+; Gly is hydrogen bonded to the gamma phosphate of GTP through the backbone amide - G4 box - G5 box > d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd04164 - GTP/Mg2+ binding site - Switch I region (i.e. effector region) ~ conformation change upon GTP binding - Switch II region ~ conformation change upon GTP binding - G1 box (i.e. P-loop or the Walker A motif) ~ signature motif of phosphate-binding loop - G2 box motif: T ~ G2 overlaps with the Switch I region - G3 box ~ overlaps the Switch II region, which includes the Walker B motif; Asp forms a water-bridged contact with Mg2+; Gly is hydrogen bonded to the gamma phosphate of GTP through the backbone amide - G4 box - G5 box ----------------------------------- ----------------------------------- #2 a.4 Ancestry = 0.006 > d1lvaa1 a.4.5.35 (A:377-437) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} - Pfam ID = pfam09105 - DNA and RNA binding > d1lvaa2 a.4.5.35 (A:438-510) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} - Pfam ID = pfam09106 - DNA and RNA binding > d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} --- no domains identified --- > d1lvaa4 a.4.5.35 (A:575-634) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} - Pfam ID = pfam09107 - DNA and RNA binding > d1j5er_ a.4.8.1 (R:) Ribosomal protein S18 {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cl00373 - Ribosomal_S18 Super-family > d1mmsa1 a.4.7.1 (A:71-140) Ribosomal protein L11, C-terminal domain {Thermotoga maritima [TaxId: 2336]} > d1yhqi1 a.4.7.1 (I:66-135) Ribosomal protein L11, C-terminal domain {Archaeon Haloarcula marismortui [TaxId: 2238]} - NCBI Conserved Domain ID = cd00349 - L11 and 23S rRNA form an essential part of the GTPase-associated region (GAR) - proposed to play a significant role in the binding of initiation factors, elongation factors, and release factors to the ribosome - 23S rRNA interface - L7/L12 interface - L25 interface - putative thiostrepton binding site > d1rq6a_ a.4.15.1 (A:) ribosomal protein S17e {Methanobacterium thermoautotrophicum [TaxId: 145262]} - NCBI Conserved Domain ID = cl00610 - Ribosomal_S17e ----------------------------------- ----------------------------------- #3 d.58 Ancestry = 0.013 > d1gh8a_ d.58.12.1 (A:) aEF-1beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} - NCBI Conserved Domain ID = cd00292 - EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP - EF1A binds to and delivers the aminoacyl tRNA to the ribosome - EF1A interaction surface ~ GDP/GTP exchange is induced by disruption of Mg binding site of EF1A by insertion of N terminal lysine > d2bv3a4 d.58.11.1 (A:404-478) Elongation factor G (EF-G) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = PRK00007 - promotes GTP-dependent translocation of the ribosome during translation > d1jjcb4 d.58.13.1 (B:682-785) Phenylalanyl-tRNA synthetase {Thermus thermophilus [TaxId: 274]} - Pfam ID = pfam03147 - Ferredoxin-fold anticodon binding domain - domain found in some phenylalanyl tRNA synthetases > d1j5ej_ d.58.15.1 (J:) Ribosomal protein S10 {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cl00314 - This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes > d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} > d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} - NCBI Conserved Domain ID = cl00414 - Ribosomal protein S6 - Pfam ID = pfam07541 - Eukaryotic translation initiation factor 2 alpha subunit - These proteins share a region of similarity that falls towards the C terminus from pfam00575. > d2ahob3 d.58.51.1 (B:176-264) eIF-2-alpha, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} - Pfam ID = pfam07541 - Eukaryotic translation initiation factor 2 alpha subunit - These proteins share a region of similarity that falls towards the C terminus from pfam00575 > d1r89a3 d.58.16.2 (A:258-437) tRNA nucleotidyltransferase, C-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} - NCBI Conserved Domain ID = PRK13300 - tRNA CCA-pyrophosphorylase; Provisional - catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA - does not have phosphohydrolase activity ----------------------------------- ----------------------------------- #4 c.1 Ancestry = 0.019 > d1r5ya_ c.1.20.1 (A:) Queosine tRNA-guanine transglycosylase {Zymomonas mobilis [TaxId: 542]} > d1iq8a1 c.1.20.1 (A:6-360) Archaeosine tRNA-guanine transglycosylase, N-terminal domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} - NCBI Conserved Domain ID = cl00409 - also known as tRNA-guanine transglycosylase and guanine insertion enzyme - modifies tRNAs for asparagine, aspartic acid, histidine and tyrosine with queuine - catalyses the exchange of guanine-34 at the wobble position with 7-aminomethyl-7-deazaguanine, and the addition of a cyclopentenediol moiety to 7-aminomethyl-7-deazaguanine-34 tRNA - zinc binding motif - tRNA and 7-aminomethyl-7deazaguanine binding residues > d1vhna_ c.1.4.1 (A:) Putative flavin oxidoreducatase TM0096 {Thermotoga maritima [TaxId: 2336]} - NCBI Conserved Domain ID = cd02801 - Dihydrouridine synthase-like (DUS-like) FMN-binding domain - catalyze the reduction of the 5,6-double bond of a uridine residue on tRNA - widely observed in prokaryotes and eukaryotes, and also in some archaea - role of dihydrouridine in tRNA is currently unknown, but may increase conformational flexibility of the tRNA - active site ~ the sulfate ion is thought to be coincident with the natural ligand binding site ----------------------------------- ----------------------------------- #5 c.2 Ancestry = 0.025 > d1gpja2 c.2.1.7 (A:144-302) Glutamyl tRNA-reductase middle domain {Archaeon Methanopyrus kandleri [TaxId: 2320]} ***ASSOCIATED WITH TETRAPYROLE SYNTHESIS, NOT TRANSLATION*** - NCBI Conserved Domain ID = cd05213 - NADP-binding domain of glutamyl-tRNA reductase - catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde ----------------------------------- ----------------------------------- #6 c.23 Ancestry = 0.031 > d1j5eb_ c.23.15.1 (B:) Ribosomal protein S2 {Thermus thermophilus [TaxId: 274]} > d1vi6a_ c.23.15.1 (A:) Ribosomal protein S2 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} *** Moonlighting Protein *** - NCBI Conserved Domain ID = cd01425 - Ribosomal protein S2 (RPS2) - might contact the messenger RNA and several components of the ribosome - in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit - also functions as the 67 kDa laminin receptor (LAMR1 or 67LR) s a cell surface receptor which interacts with a variety of ligands - rRNA interaction site ~ contacts 16s rRNA in the 30s ribosomal subunit - S8 interaction site ~ contacts ribosomal protein S8 in the 30s subunit ----------------------------------- ----------------------------------- #7 c.55 0.038 > d1ilya_ c.55.4.1 (A:) Ribosomal protein L18 (L18p) {Thermus thermophilus [TaxId: 274]} > d1jj2m_ c.55.4.1 (M:) Ribosomal protein L18 (L18p) {Archaeon Haloarcula marismortui [TaxId: 2238]} - NCBI Conserved Domain ID = cd00432 - Ribosomal L18/L5e protein - L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA - one of the last steps in ribosome assembly - 5S rRNA interface - 23S rRNA interface - L21e interface - L27 interface - L5 interface > d1j5ek_ c.55.4.1 (K:) Ribosomal protein S11 {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cl00332 - plays an essential role in selecting the correct tRNA in protein biosynthesis - located on the large lobe of the small ribosomal subunit > d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd06142 - Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA - catalytic site ~ four negatively charged residues (DEDD) that serve as ligands for the two metal (Zn) ions required for activity - putative active site ~ binds ssDNA or RNA substrate ----------------------------------- ----------------------------------- #8 b.40 Ancestry = 0.044 > d1bkba2 b.40.4.5 (A:75-139) C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} - NCBI Conserved Domain ID = cd04467 - Archaeal translation Initiation Factor 5A (aIF5A) - only protein known to have unusual amino acid hypusine - eIF5A interacts with components of the 80S ribosome and translation elongation factors 2 - prefers to bind actively translating ribosome > d1khia2 b.40.4.5 (A:103-173) C-terminal domain of eIF5a homologue (Hex1) {Filamentous fungi (Neurospora crassa) [TaxId: 5141]} ***ASSOCIATED WITH WORONIN BODY, NOT TRANSLATION*** - NCBI Conserved Domain ID = cd04469 - The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A) - sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A) > d1x6oa2 b.40.4.5 (A:87-165) C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) {Leishmania infantum [TaxId: 5671]} - NCBI Conserved Domain ID = cd04468 - Eukaryotic translation Initiation Factor 5A (eIF5A) - interacts with components of the 80S ribosome and translation elongation factors 2 (eEF2) - C-terminal S1 domain resembles the oligonucleotides-binding fold (OB fold) which binds RNA - eIF5A prefers binding to the actively translating ribosome > d1ueba2 b.40.4.5 (A:64-126) Elongation factor P middle and C-terminal domains {Thermus thermophilus HB8 [TaxId: 300852]} > d1ueba3 b.40.4.5 (A:127-184) Elongation factor P middle and C-terminal domains {Thermus thermophilus HB8 [TaxId: 300852]} - NCBI Conserved Domain ID = cd04470 - Domain II of translation elongation factor P (EF-P) stimulates the peptidyltransferase activity in the prokaryotic 70S ribosome - binds to both the 30S and 50S ribosomal subunits - EF-P interacts with domains 2 and 5 of the 23S rRNA > d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]} - NCBI Conserved Domain ID = cd04316 - N-terminal, anticodon recognition domain of the type found in the homodimeric non-discriminating (ND) Pyrococcus kodakaraensis aspartyl-tRNA synthetase (AspRS) - i) the activation the AA by ATP in the presence of magnesium ions, followed by - ii) the transfer of the activated AA to the terminal ribose of tRNA - P. kodakaraensis ND-AspRS can charge both tRNAAsp and tRNAAsn > d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]} > d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]} - NCBI Conserved Domain ID = cd04317 - N-terminal, anticodon recognition domain found in Escherichia coli aspartyl-tRNA synthetase (AspRS), the human mitochondrial (mt) AspRS-2, the discriminating (D) Thermus thermophilus AspRS-1, and the nondiscriminating (ND) Helicobacter pylori AspRS. > d1jjcb3 b.40.4.4 (B:39-151) Domain B2 of PheRS-beta, PheT {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd02796 - tRNA-binding-domain-containing prokaryotic phenylalanly tRNA synthetase (PheRS) beta chain - PheRSs belong structurally to class II aminoacyl tRNA synthetases (aaRSs) but, as they aminoacylate the 2'OH of the terminal ribose of tRNA they belong functionally to class 1 aaRSs - This domain has general tRNA binding properties and is believed to direct tRNAphe to the active site of the enzyme. > d1hr0w_ b.40.4.5 (W:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd04451 - Translation Initiation Factor IF1, S1-like RNA-binding domain - IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3 - IF1 may contribute to the fidelity of the selection of the initiation site of the mRNA. > d1jt8a_ b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Archaeon Methanococcus jannaschii [TaxId: 2190]} - NCBI Conserved Domain ID = cd04451 - Translation initiation factor IF1A-like, S1-like RNA-binding domain - eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA - Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon > d1pyba_ b.40.4.4 (A:) Structure-specific tRNA-binding protein TRBP111 {Aquifex aeolicus [TaxId: 63363]} - NCBI Conserved Domain ID = cd02800 - tRNA-binding-domain-containing Escherichia coli methionyl-tRNA synthetase (EcMetRS)-like proteins - structure-specific molecular chaperone recognizing the L-shape of the tRNA fold - this domain acts as the dimerization domain > d1j5el_ b.40.4.5 (L:) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd03368 - S12 is located at the interface of the large and small ribosomal subunits of prokaryotes, chloroplasts and mitochondria - essential for maintenance of a pretranslocation state - together with S13, functions as a control element for the rRNA- and tRNA-driven movements of translocation - Antibiotics such as streptomycin bind S12 and cause the ribosome to misread the genetic code. > d1j5eq_ b.40.4.5 (Q:) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]} - Pfam ID = pfam00366 - ribosomal subunit protein S17 is known to bind specifically to the 5' end of 16S ribosomal RNA in Escherichia coli - thought to be involved in the recognition of termination codons > d1jj2a2 b.40.4.5 (A:1-90) N-terminal domain of ribosomal protein L2 {Archaeon Haloarcula marismortui [TaxId: 2238]} > d1rl2a2 b.40.4.5 (A:60-125) N-terminal domain of ribosomal protein L2 {Bacillus stearothermophilus [TaxId: 1422]} - Pfam ID = pfam00181 - L2 is one of the proteins from the large ribosomal subunit - L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity > d1ne3a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} - NCBI Conserved Domain ID = cd04457 - S28E, S1-like RNA-binding domain - S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins - S28E protein is a component of the 30S ribosomal subunit - S28E may control precursor RNA splicing and turnover in mRNA maturation process but its function in the ribosome is largely unknown > d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} - NCBI Conserved Domain ID = cd04452 - The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain - The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon - The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP - The IF2a subunit is a major site of control of the translation initiation process, via phosphorylation of a specific serine residue ----------------------------------- ----------------------------------- #9 c.66 Ancestry = 0.050 > d2b3ta1 c.66.1.30 (A:2-275) N5-glutamine methyltransferase, HemK {Escherichia coli [TaxId: 562]} > d1im8a_ c.66.1.14 (A:) Hypothetical protein HI0319 (YecO) {Haemophilus influenzae [TaxId: 727]} > d1i9ga_ c.66.1.13 (A:) Probable methyltransferase Rv2118c {Mycobacterium tuberculosis [TaxId: 1773]} > d1o54a_ c.66.1.13 (A:) Hypothetical protein TM0748 {Thermotoga maritima [TaxId: 2336]} > d1yzha1 c.66.1.53 (A:8-211) tRNA (guanine-N(7)-)-methyltransferase TrmB {Streptococcus pneumoniae [TaxId: 1313]} - NCBI Conserved Domain ID = cd02440 - S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I - AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy) > d1yb2a1 c.66.1.13 (A:6-255) Hypothetical protein Ta0852 {Thermoplasma acidophilum [TaxId: 2303]} > d1g8aa_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Pyrococcus horikoshii [TaxId: 53953]} > d1nt2a_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} - NCBI Conserved Domain ID = cl09931 - Rossmann-fold NAD(P)(+)-binding proteins - exhibits a consensus binding pattern similar to GXGXXG, in which the first 2 glycines participate in NAD(P)-binding, and the third facilitates close packing of the helix to the beta-strand ----------------------------------- ----------------------------------- #10 c.26 0.057 > d1irxa2 c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {Archaeon Pyrococcus horikoshii [TaxId: 53953]} - NCBI Conserved Domain ID = cd00674 - catalytic core domain of lysyl tRNA synthetase (LysRS) - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding - active site ~ ATP and tRNA binding sites added based on similarity to GluRS, tRNA is required for amino acid activation - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1gtra2 c.26.1.1 (A:8-338) Glutaminyl-tRNA synthetase (GlnRS) {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd00807 - split domain - Glutaminyl-tRNA synthetase (GlnRS) and non-descriminating Glutamyl-tRNA synthetase (GluRS) cataytic core domain - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site ~ tRNA is required for amino acid activation - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1u0bb2 c.26.1.1 (B:1-315) Cysteinyl-tRNA synthetase (CysRS) {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd00672 - split domain - catalytic core domain of cysteinyl tRNA synthetase (CysRS) - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site, KMSKS loop is in the open confromation in the absence of bound ATP or cysteinyl adenylate - core domain > d1ffya3 c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus aureus [TaxId: 1280]} > d1ilea3 c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthetase (IleRS) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd00818 - catalytic core domain of isoleucine amino-acyl tRNA synthetases (IleRS) - core domain is involved in fidelity - active site - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site, KMSKS loop is in the open confromation in the absence of bound ATP or cysteinyl adenylate - core domain ~ subject to both deletions and rearrangements, this editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids > d1iq0a2 c.26.1.1 (A:97-466) Arginyl-tRNA synthetase (ArgRS) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd00671 - catalytic core domain of Arginyl tRNA synthetase (ArgRS) - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site ~ tRNA is required for amino acid activation - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site, this motif is absent in a subgroup of ArgRS's > d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd00817 - catalytic core domain of valine amino-acyl tRNA synthetases (ValRS) - ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements - core domain insertion region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. - active site - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1h3na3 c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetase (LeuRS) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd00812 - catalytic core domain of leucyl tRNA synthetase (LeuRS) - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - core domain insertion region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids. - active site - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1h3fa1 c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophilus [TaxId: 274]} > d1j1ua_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanococcus jannaschii [TaxId: 2190]} > d1jila_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus aureus [TaxId: 1280]} - NCBI Conserved Domain ID = cd00805 - Tyrosinyl-tRNA synthetase (TyrRS) catalytic core domain - TyrRS is a homodimer - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site - dimer interface - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1i6la_ c.26.1.1 (A:) Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus stearothermophilus [TaxId: 1422]} - NCBI Conserved Domain ID = cd00806 - TrpRS is a homodimer - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site - dimer interface - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1j09a2 c.26.1.1 (A:1-305) Glutamyl-tRNA synthetase (GluRS) {Thermus thermophilus [TaxId: 274]} > d1nzja_ c.26.1.1 (A:) Glutamyl-Q tRNA-Asp synthetase YadB {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd00808 - Descriminating Glutamyl-tRNA synthetase (GluRS) catalytic core domain - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - active site ~ tRNA is required for amino acid activation - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site > d1pfva2 c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthetase (MetRS) {Escherichia coli [TaxId: 562]} > d1rqga2 c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthetase (MetRS) {Pyrococcus abyssi [TaxId: 29292]} > d2d5ba2 c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetRS) {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd00814 - catalytic core domain of methionine tRNA synthetase (MetRS) - responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate - As a result of a deletion event, MetRS has a significantly shorter core domain insertion that IleRS, ValRS, and LeuR - MetRS insertion lacks the editing function - active site - HIGH motif ~ characteristic class I, involved in ATP binding, part of active site - KMSKS motif ~ characteristic class I, involved in ATP binding, part of active site - core domain > d1ni5a1 c.26.2.5 (A:0-226) tRNA-Ile-lysidine synthetase, TilS, N-terminal domain {Escherichia coli [TaxId: 562]} > d1wy5a1 c.26.2.5 (A:1-216) TilS-like protein Aq_1887 {Aquifex aeolicus [TaxId: 63363]} ***SEQUENCCE SEARCH ONLY RETRIEVED A CELL CYCLE DOMAINS*** - NCBI Conserved Domain ID = cd01992 - N-terminal domain of predicted ATPase of the PP-loop faimly implicated in cell cycle control - adenosine nucleotide binding site predicted by similar proteins ----------------------------------- ----------------------------------- ----------------------------------- ----------------------------------- ----------------------------------- ----------------------------------- ----------------------------------- ----------------------------------- REFERENCES: > d2bv3a2 c.37.1.8 (A:7-282) Elongation factor G (EF-G), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd01886 1: Sergiev PV, Bogdanov AA, Dontsova OA. How can elongation factors EF-G and EF-Tu discriminate the functional state of the ribosome using the same binding site? FEBS Lett. 2005 Oct 24;579(25):5439-42. Epub 2005 Sep 26. Review. PubMed PMID: 16213500. 2: Sagar MB, Lucast L, Doudna JA. Conserved but nonessential interaction of SRP RNA with translation factor EF-G. RNA. 2004 May;10(5):772-8. PubMed PMID: 15100432; PubMed Central PMCID: PMC1370567. 3: Wilson KS, Nechifor R. Interactions of translational factor EF-G with the bacterial ribosome before and after mRNA translocation. J Mol Biol. 2004 Mar 12;337(1):15-30. PubMed PMID: 15001349. 4: Zavialov AV, Ehrenberg M. Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell. 2003 Jul 11;114(1):113-22. PubMed PMID: 12859902. 5: Savelsbergh A, Katunin VI, Mohr D, Peske F, Rodnina MV, Wintermeyer W. An elongation factor G-induced ribosome rearrangement precedes tRNA-mRNA translocation. Mol Cell. 2003 Jun;11(6):1517-23. PubMed PMID: 12820965. 6: Kaji A, Kiel MC, Hirokawa G, Muto AR, Inokuchi Y, Kaji H. The fourth step of protein synthesis: disassembly of the posttermination complex is catalyzed by elongation factor G and ribosome recycling factor, a near-perfect mimic of tRNA. Cold Spring Harb Symp Quant Biol. 2001;66:515-29. Review. PubMed PMID: 12762054. 7: Fredrick K, Noller HF. Catalysis of ribosomal translocation by sparsomycin. Science. 2003 May 16;300(5622):1159-62. PubMed PMID: 12750524. 8: Joseph S. After the ribosome structure: how does translocation work? RNA. 2003 Feb;9(2):160-4. Review. PubMed PMID: 12554856; PubMed Central PMCID: PMC1370379. 9: Sprang SR. G protein mechanisms: insights from structural analysis. Annu Rev Biochem. 1997;66:639-78. Review. PubMed PMID: 9242920. 10: Green R. Ribosomal translocation: EF-G turns the crank. Curr Biol. 2000 May 18;10(10):R369-73. Review. PubMed PMID: 10837219. 11: Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002 Mar 15;317(1):41-72. PubMed PMID: 11916378. 12: Ganoza MC, Kiel MC, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002 Sep;66(3):460-85, table of contents. Review. PubMed PMID: 12209000; PubMed Central PMCID: PMC120792. 13: Wintermeyer W, Rodnina MV. Translational elongation factor G: a GTP-driven motor of the ribosome. Essays Biochem. 2000;35:117-29. Review. PubMed PMID: 12471894. > d2c78a3 c.37.1.8 (A:9-212) Elongation factor Tu (EF-Tu), N-terminal (G) domain {Thermus thermophilus [TaxId: 274]} - NCBI Conserved Domain ID = cd01884 1: Dahl LD, Wieden HJ, Rodnina MV, Knudsen CR. The importance of P-loop and domain movements in EF-Tu for guanine nucleotide exchange. J Biol Chem. 2006 Jul 28;281(30):21139-46. Epub 2006 May 22. PubMed PMID: 16717093. 2: Gromadski KB, Rodnina MV. Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome. Nat Struct Mol Biol. 2004 Apr;11(4):316-22. Epub 2004 Mar 7. PubMed PMID: 15004548. 3: Snyder L, Blight S, Auchtung J. Regulation of translation of the head protein of T4 bacteriophage by specific binding of EF-Tu to a leader sequence. J Mol Biol. 2003 Nov 28;334(3):349-61. PubMed PMID: 14623179. 4: Daviter T, Wieden HJ, Rodnina MV. Essential role of histidine 84 in elongation factor Tu for the chemical step of GTP hydrolysis on the ribosome. J Mol Biol. 2003 Sep 19;332(3):689-99. PubMed PMID: 12963376. 5: Zavialov AV, Ehrenberg M. Peptidyl-tRNA regulates the GTPase activity of translation factors. Cell. 2003 Jul 11;114(1):113-22. PubMed PMID: 12859902. 6: Mohr D, Wintermeyer W, Rodnina MV. GTPase activation of elongation factors Tu and G on the ribosome. Biochemistry. 2002 Oct 15;41(41):12520-8. PubMed PMID: 12369843. 7: Ganoza MC, Kiel MC, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002 Sep;66(3):460-85, table of contents. Review. PubMed PMID: 12209000; PubMed Central PMCID: PMC120792. 8: Ohtsuki T, Sato A, Watanabe Y, Watanabe K. A unique serine-specific elongation factor Tu found in nematode mitochondria. Nat Struct Biol. 2002 Sep;9(9):669-73. Erratum in: Nat Struct Biol. 2003 Aug;10(8):669. PubMed PMID: 12145639. 9: Krab IM, Parmeggiani A. Mechanisms of EF-Tu, a pioneer GTPase. Prog Nucleic Acid Res Mol Biol. 2002;71:513-51. Review. PubMed PMID: 12102560. 10: Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002 Mar 15;317(1):41-72. PubMed PMID: 11916378. 11: Asahara H, Uhlenbeck OC. The tRNA specificity of Thermus thermophilus EF-Tu. Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3499-504. Epub 2002 Mar 12. PubMed PMID: 11891293; PubMed Central PMCID: PMC122552. 12: Stark H, Rodnina MV, Rinke-Appel J, Brimacombe R, Wintermeyer W, van Heel M. Visualization of elongation factor Tu on the Escherichia coli ribosome. Nature. 1997 Sep 25;389(6649):403-6. PubMed PMID: 9311785. 13: Sprang SR. G protein mechanisms: insights from structural analysis. Annu Rev Biochem. 1997;66:639-78. Review. PubMed PMID: 9242920. > d1wb1a4 c.37.1.8 (A:1-179) Elongation factor SelB, N-terminal domain {Methanococcus maripaludis [TaxId: 39152]} - NCBI Conserved Domain ID = cd01889 1: Leibundgut M, Frick C, Thanbichler M, Bck A, Ban N. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J. 2005 Jan 12;24(1):11-22. Epub 2004 Dec 23. PubMed PMID: 15616587; PubMed Central PMCID: PMC544917. 2: Lescure A, Fagegaltier D, Carbon P, Krol A. Protein factors mediating selenoprotein synthesis. Curr Protein Pept Sci. 2002 Feb;3(1):143-51. Review. PubMed PMID: 12370018. 3: Thanbichler M, Bck A. Functional analysis of prokaryotic SELB proteins. Biofactors. 2001;14(1-4):53-9. Review. PubMed PMID: 11568440. 4: Rother M, Resch A, Wilting R, Bck A. Selenoprotein synthesis in archaea. Biofactors. 2001;14(1-4):75-83. Review. PubMed PMID: 11568443. 5: Romero H, Zhang Y, Gladyshev VN, Salinas G. Evolution of selenium utilization traits. Genome Biol. 2005;6(8):R66. Epub 2005 Jul 27. PubMed PMID: 16086848; PubMed Central PMCID: PMC1273633. 6: Yoshizawa S, Rasubala L, Ose T, Kohda D, Fourmy D, Maenaka K. Structural basis for mRNA recognition by elongation factor SelB. Nat Struct Mol Biol. 2005 Feb;12(2):198-203. Epub 2005 Jan 23. PubMed PMID: 15665870. 7: Keeling PJ, Fast NM, McFadden GI. Evolutionary relationship between translation initiation factor eIF-2gamma and selenocysteine-specific elongation factor SELB: change of function in translation factors. J Mol Evol. 1998 Dec;47(6):649-55. PubMed PMID: 9847405. 8: Ganoza MC, Kiel MC, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002 Sep;66(3):460-85, table of contents. Review. PubMed PMID: 12209000; PubMed Central PMCID: PMC120792. 9: Sprang SR. G protein mechanisms: insights from structural analysis. Annu Rev Biochem. 1997;66:639-78. Review. PubMed PMID: 9242920. 10: Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002 Mar 15;317(1):41-72. PubMed PMID: 11916378. > d1g7sa4 c.37.1.8 (A:1-227) Initiation factor IF2/eIF5b, N-terminal (G) domain {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} - NCBI Conserved Domain ID = cd01887 1: Acker MG, Shin BS, Dever TE, Lorsch JR. Interaction between eukaryotic initiation factors 1A and 5B is required for efficient ribosomal subunit joining. J Biol Chem. 2006 Mar 31;281(13):8469-75. Epub 2006 Feb 3. PubMed PMID: 16461768. 2: Guillon L, Schmitt E, Blanquet S, Mechulam Y. Initiator tRNA binding by e/aIF5B, the eukaryotic/archaeal homologue of bacterial initiation factor IF2. Biochemistry. 2005 Nov 29;44(47):15594-601. PubMed PMID: 16300409. 3: Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M. The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. EMBO J. 2003 Oct 15;22(20):5593-601. PubMed PMID: 14532131; PubMed Central PMCID: PMC213779. 4: Marintchev A, Kolupaeva VG, Pestova TV, Wagner G. Mapping the binding interface between human eukaryotic initiation factors 1A and 5B: a new interaction between old partners. Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1535-40. Epub 2003 Feb 4. PubMed PMID: 12569173; PubMed Central PMCID: PMC149867. 5: Shin BS, Maag D, Roll-Mecak A, Arefin MS, Burley SK, Lorsch JR, Dever TE. Uncoupling of initiation factor eIF5B/IF2 GTPase and translational activities by mutations that lower ribosome affinity. Cell. 2002 Dec 27;111(7):1015-25. PubMed PMID: 12507428. 6: Lee JH, Pestova TV, Shin BS, Cao C, Choi SK, Dever TE. Initiation factor eIF5B catalyzes second GTP-dependent step in eukaryotic translation initiation. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16689-94. Epub 2002 Dec 6. PubMed PMID: 12471154; PubMed Central PMCID: PMC139205. 7: Ganoza MC, Kiel MC, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002 Sep;66(3):460-85, table of contents. Review. PubMed PMID: 12209000; PubMed Central PMCID: PMC120792. 8: Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002 Mar 15;317(1):41-72. PubMed PMID: 11916378. 9: Roll-Mecak A, Shin BS, Dever TE, Burley SK. Engaging the ribosome: universal IFs of translation. Trends Biochem Sci. 2001 Dec;26(12):705-9. PubMed PMID: 11738593. 10: Choi SK, Olsen DS, Roll-Mecak A, Martung A, Remo KL, Burley SK, Hinnebusch AG, Dever TE. Physical and functional interaction between the eukaryotic orthologs of prokaryotic translation initiation factors IF1 and IF2. Mol Cell Biol. 2000 Oct;20(19):7183-91. PubMed PMID: 10982835; PubMed Central PMCID: PMC86272. 11: Pestova TV, Lomakin IB, Lee JH, Choi SK, Dever TE, Hellen CU. The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature. 2000 Jan 20;403(6767):332-5. PubMed PMID: 10659855. 12: Sprang SR. G protein mechanisms: insights from structural analysis. Annu Rev Biochem. 1997;66:639-78. Review. PubMed PMID: 9242920. > d2gj8a1 c.37.1.8 (A:216-376) Probable tRNA modification GTPase TrmE (MnmE), G domain {Escherichia coli [TaxId: 562]} - NCBI Conserved Domain ID = cd04164 1: Yim L, Martnez-Vicente M, Villarroya M, Aguado C, Knecht E, Armengod ME. The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE protein are essential for its tRNA modifying function. J Biol Chem. 2003 Aug 1;278(31):28378-87. Epub 2003 Apr 30. PubMed PMID: 12730230. 2: Gong S, Ma Z, Foster JW. The Era-like GTPase TrmE conditionally activates gadE and glutamate-dependent acid resistance in Escherichia coli. Mol Microbiol. 2004 Nov;54(4):948-61. PubMed PMID: 15522079. 3: Morimoto T, Loh PC, Hirai T, Asai K, Kobayashi K, Moriya S, Ogasawara N. Six GTP-binding proteins of the Era/Obg family are essential for cell growth in Bacillus subtilis. Microbiology. 2002 Nov;148(Pt 11):3539-52. PubMed PMID: 12427945. 4: Mittenhuber G. Comparative genomics of prokaryotic GTP-binding proteins (the Era, Obg, EngA, ThdF (TrmE), YchF and YihA families) and their relationship to eukaryotic GTP-binding proteins (the DRG, ARF, RAB, RAN, RAS and RHO families). J Mol Microbiol Biotechnol. 2001 Jan;3(1):21-35. Review. PubMed PMID: 11200227. 5: Leipe DD, Wolf YI, Koonin EV, Aravind L. Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol. 2002 Mar 15;317(1):41-72. PubMed PMID: 11916378. 6: Pandit SB, Srinivasan N. Survey for g-proteins in the prokaryotic genomes: prediction of functional roles based on classification. Proteins. 2003 Sep 1;52(4):585-97. PubMed PMID: 12910458. 7: Caldon CE, March PE. Function of the universally conserved bacterial GTPases. Curr Opin Microbiol. 2003 Apr;6(2):135-9. Review. PubMed PMID: 12732302. 8: Caldon CE, Yoong P, March PE. Evolution of a molecular switch: universal bacterial GTPases regulate ribosome function. Mol Microbiol. 2001 Jul;41(2):289-97. Review. PubMed PMID: 11489118. ----------------------------------- ----------------------------------- #2 a.4 Ancestry = 0.006 > d1lvaa1 a.4.5.35 (A:377-437) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} > d1lvaa2 a.4.5.35 (A:438-510) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} > d1lvaa3 a.4.5.35 (A:511-574) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} > d1lvaa4 a.4.5.35 (A:575-634) C-terminal fragment of elongation factor SelB {Moorella thermoacetica [TaxId: 1525]} 1: Selmer M, Su XD. Crystal structure of an mRNA-binding fragment of Moorella thermoacetica elongation factor SelB. EMBO J. 2002 Aug 1;21(15):4145-53. PubMed PMID: 12145214; PubMed Central PMCID: PMC126154. > d1j5er_ a.4.8.1 (R:) Ribosomal protein S18 {Thermus thermophilus [TaxId: 274]} 1: Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science. 2000 Apr 7;288(5463):107-13. PubMed PMID: 10753109. 2: Schnier J, Kitakawa M, Isono K. The nucleotide sequence of an Escherichia coli chromosomal region containing the genes for ribosomal proteins S6, S18, L9 and an open reading frame. Mol Gen Genet. 1986 Jul;204(1):126-32. PubMed PMID: 3528756. > d1mmsa1 a.4.7.1 (A:71-140) Ribosomal protein L11, C-terminal domain {Thermotoga maritima [TaxId: 2336]} > d1yhqi1 a.4.7.1 (I:66-135) Ribosomal protein L11, C-terminal domain {Archaeon Haloarcula marismortui [TaxId: 2238]} 1: Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P. Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin. Mol Cell. 2008 Apr 11;30(1):26-38. PubMed PMID: 18406324. 2: Chandramouli P, Topf M, Mntret JF, Eswar N, Cannone JJ, Gutell RR, Sali A, Akey CW. Structure of the mammalian 80S ribosome at 8.7 A resolution. Structure. 2008 Apr;16(4):535-48. PubMed PMID: 18400176. 3: Kavran JM, Steitz TA. Structure of the base of the L7/L12 stalk of the Haloarcula marismortui large ribosomal subunit: analysis of L11 movements. J Mol Biol. 2007 Aug 24;371(4):1047-59. Epub 2007 Jun 4. PubMed PMID: 17599351. 4: Jonker HR, Ilin S, Grimm SK, Whnert J, Schwalbe H. L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy. Nucleic Acids Res. 2007;35(2):441-54. Epub 2006 Dec 14. PubMed PMID: 17169991; PubMed Central PMCID: PMC1802607. 5: Jenvert RM, Schiavone LH. The flexible N-terminal domain of ribosomal protein L11 from Escherichia coli is necessary for the activation of stringent factor. J Mol Biol. 2007 Jan 19;365(3):764-72. Epub 2006 Oct 25. PubMed PMID: 17095013. 6: Kasai K, Nishizawa T, Takahashi K, Hosaka T, Aoki H, Ochi K. Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J Bacteriol. 2006 Oct;188(20):7111-22. PubMed PMID: 17015650; PubMed Central PMCID: PMC1636220. 7: Dai MS, Shi D, Jin Y, Sun XX, Zhang Y, Grossman SR, Lu H. Regulation of the MDM2-p53 pathway by ribosomal protein L11 involves a post-ubiquitination mechanism. J Biol Chem. 2006 Aug 25;281(34):24304-13. Epub 2006 Jun 27. PubMed PMID: 16803902; PubMed Central PMCID: PMC1783840. 8: Bouakaz L, Bouakaz E, Murgola EJ, Ehrenberg M, Sanyal S. The role of ribosomal protein L11 in class I release factor-mediated translation termination and translational accuracy. J Biol Chem. 2006 Feb 17;281(7):4548-56. Epub 2005 Dec 21. PubMed PMID: 16371360. 9: Bowen WS, Van Dyke N, Murgola EJ, Lodmell JS, Hill WE. Interaction of thiostrepton and elongation factor-G with the ribosomal protein L11-binding domain. J Biol Chem. 2005 Jan 28;280(4):2934-43. Epub 2004 Oct 18. PubMed PMID: 15492007. 10: Klein DJ, Moore PB, Steitz TA. The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol. 2004 Jun 25;340(1):141-77. PubMed PMID: 15184028. 11: Bhat KP, Itahana K, Jin A, Zhang Y. Essential role of ribosomal protein L11 in mediating growth inhibition-induced p53 activation. EMBO J. 2004 Jun 16;23(12):2402-12. Epub 2004 May 20. PubMed PMID: 15152193; PubMed Central PMCID: PMC423289. 12: Lentzen G, Klinck R, Matassova N, Aboul-ela F, Murchie AI. Structural basis for contrasting activities of ribosome binding thiazole antibiotics. Chem Biol. 2003 Aug;10(8):769-78. PubMed PMID: 12954336. 13: Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell. 2001 Nov 30;107(5):679-88. PubMed PMID: 11733066. 14: Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA. Placement of protein and RNA structures into a 5 A-resolution map of the 50S ribosomal subunit. Nature. 1999 Aug 26;400(6747):841-7. PubMed PMID: 10476961. 15: Wimberly BT, Guymon R, McCutcheon JP, White SW, Ramakrishnan V. A detailed view of a ribosomal active site: the structure of the L11-RNA complex. Cell. 1999 May 14;97(4):491-502. PubMed PMID: 10338213. > d1rq6a_ a.4.15.1 (A:) ribosomal protein S17e {Methanobacterium thermoautotrophicum [TaxId: 145262]} 1: Oura CA, Kinnaird J, Tait A, Shiels BR. Identification of a 40S Ribosomal protein (S17) that is differentially expressed between the macroschizont and piroplasm stages of Theileria annulata. Int J Parasitol. 2002 Jan;32(1):73-80. PubMed PMID: 11796124. 2: Simitsopoulou M, Avila H, Franceschi F. Ribosomal gene disruption in the extreme thermophile Thermus thermophilus HB8. Generation of a mutant lacking ribosomal protein S17. Eur J Biochem. 1999 Dec;266(2):524-32. PubMed PMID: 10561594. 3: Teem JL, Rodriguez JR, Tung L, Rosbash M. The rna2 mutation of yeast affects the processing of actin mRNA as well as ribosomal protein mRNAs. Mol Gen Genet. 1983;192(1-2):101-3. PubMed PMID: 6358792. 4: Abovich N, Rosbash M. Two genes for ribosomal protein 51 of Saccharomyces cerevisiae complement and contribute to the ribosomes. Mol Cell Biol. 1984 Sep;4(9):1871-9. PubMed PMID: 6092944; PubMed Central PMCID: PMC368997. ----------------------------------- ----------------------------------- #3 d.58 Ancestry = 0.013 > d1gh8a_ d.58.12.1 (A:) aEF-1beta {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} 1: Wilson KS, Noller HF. Molecular movement inside the translational engine. Cell. 1998 Feb 6;92(3):337-49. Review. PubMed PMID: 9476894. 2: Ganoza MC, Kiel MC, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002 Sep;66(3):460-85, table of contents. Review. PubMed PMID: 12209000; PubMed Central PMCID: PMC120792. > d2bv3a4 d.58.11.1 (A:404-478) Elongation factor G (EF-G) {Thermus thermophilus [TaxId: 274]} 1: Datta PP, Sharma MR, Qi L, Frank J, Agrawal RK. Interaction of the G' domain of elongation factor G and the C-terminal domain of ribosomal protein L7/L12 during translocation as revealed by cryo-EM. Mol Cell. 2005 Dec 9;20(5):723-31. PubMed PMID: 16337596. 2: Peske F, Savelsbergh A, Katunin VI, Rodnina MV, Wintermeyer W. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation. J Mol Biol. 2004 Nov 5;343(5):1183-94. PubMed PMID: 15491605. 3: Agrawal RK, Penczek P, Grassucci RA, Frank J. Visualization of elongation factor G on the Escherichia coli 70S ribosome: the mechanism of translocation. Proc Natl Acad Sci U S A. 1998 May 26;95(11):6134-8. PubMed PMID: 9600930; PubMed Central PMCID: PMC27598. > d1jjcb4 d.58.13.1 (B:682-785) Phenylalanyl-tRNA synthetase {Thermus thermophilus [TaxId: 274]} 1: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 2: Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M. The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Structure. 1997 Jan 15;5(1):59-68. PubMed PMID: 9016717. > d1j5ej_ d.58.15.1 (J:) Ribosomal protein S10 {Thermus thermophilus [TaxId: 274]} 1: Greive SJ, Lins AF, von Hippel PH. Assembly of an RNA-protein complex. Binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in Escherichia coli. J Biol Chem. 2005 Oct 28;280(43):36397-408. Epub 2005 Aug 18. PubMed PMID: 16109710. 2: Hermann-Le Denmat S, Sipiczki M, Thuriaux P. Suppression of yeast RNA polymerase III mutations by the URP2 gene encoding a protein homologous to the mammalian ribosomal protein S20. J Mol Biol. 1994 Jul 1;240(1):1-7. PubMed PMID: 8021936. 3: Court DL, Patterson TA, Baker T, Costantino N, Mao X, Friedman DI. Structural and functional analyses of the transcription-translation proteins NusB and NusE. J Bacteriol. 1995 May;177(9):2589-91. PubMed PMID: 7730297; PubMed Central PMCID: PMC176924. 4: Yaguchi M, Roy C, Wittmann HG. The primary structure of protein S10 from the small ribosomal subunit of Escherichia coli. FEBS Lett. 1980 Nov 17;121(1):113-6. PubMed PMID: 7007073. 5: Parsons GD, Mackie GA. Expression of the gene for ribosomal protein S20: effects of gene dosage. J Bacteriol. 1983 Apr;154(1):152-60. PubMed PMID: 6187728; PubMed Central PMCID: PMC217442. 6: Zurawski G, Zurawski SM. Structure of the Escherichia coli S10 ribosomal protein operon. Nucleic Acids Res. 1985 Jun 25;13(12):4521-6. PubMed PMID: 3892488; PubMed Central PMCID: PMC321803. > d1loua_ d.58.14.1 (A:) Ribosomal protein S6 {Thermus thermophilus [TaxId: 274]} > d1vmba_ d.58.14.1 (A:) Ribosomal protein S6 {Thermotoga maritima [TaxId: 2336]} 1: Agalarov SC, Sridhar Prasad G, Funke PM, Stout CD, Williamson JR. Structure of the S15,S6,S18-rRNA complex: assembly of the 30S ribosome central domain. Science. 2000 Apr 7;288(5463):107-13. PubMed PMID: 10753109. 2: Otzen DE, Kristensen O, Proctor M, Oliveberg M. Structural changes in the transition state of protein folding: alternative interpretations of curved chevron plots. Biochemistry. 1999 May 18;38(20):6499-511. PubMed PMID: 10350468. 3: Thies FL, Hartung HP, Giegerich G. Cloning and expression of the Campylobacter jejuni lon gene detected by RNA arbitrarily primed PCR. FEMS Microbiol Lett. 1998 Aug 15;165(2):329-34. PubMed PMID: 9742705. 4: Lindahl M, Svensson LA, Liljas A, Sedelnikova SE, Eliseikina IA, Fomenkova NP, Nevskaya N, Nikonov SV, Garber MB, Muranova TA, et al. Crystal structure of the ribosomal protein S6 from Thermus thermophilus. EMBO J. 1994 Mar 15;13(6):1249-54. PubMed PMID: 8137808; PubMed Central PMCID: PMC394938. 5: Hitz H, Schfer D, Wittmann-Liebold B. Determination of the complete amino-acid sequence of protein S6 from the wild-type and a mutant of Escherichia coli. Eur J Biochem. 1977 May 16;75(2):497-512. PubMed PMID: 328274. > d2ahob3 d.58.51.1 (B:176-264) eIF-2-alpha, C-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} 1: Dhaliwal S, Hoffman DW. The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2alpha) from Saccharomyces cerevisiae provides a view of the loop containing serine 51, the target of the eIF2alpha-specific kinases. J Mol Biol. 2003 Nov 21;334(2):187-95. PubMed PMID: 14607111. 2: Antoun A, Pavlov MY, Andersson K, Tenson T, Ehrenberg M. The roles of initiation factor 2 and guanosine triphosphate in initiation of protein synthesis. EMBO J. 2003 Oct 15;22(20):5593-601. PubMed PMID: 14532131; PubMed Central PMCID: PMC213779. 3: Dever TE, Roll-Mecak A, Choi SK, Lee JH, Cao C, Shin BS, Burley SK. Universal translation initiation factor IF2/eIF5B. Cold Spring Harb Symp Quant Biol. 2001;66:417-24. Review. PubMed PMID: 12762044. 4: Cigan AM, Pabich EK, Feng L, Donahue TF. Yeast translation initiation suppressor sui2 encodes the alpha subunit of eukaryotic initiation factor 2 and shares sequence identity with the human alpha subunit. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2784-8. PubMed PMID: 2649894; PubMed Central PMCID: PMC287003. > d1r89a3 d.58.16.2 (A:258-437) tRNA nucleotidyltransferase, C-terminal domain {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 1: Xiong Y, Li F, Wang J, Weiner AM, Steitz TA. Crystal structures of an archaeal class I CCA-adding enzyme and its nucleotide complexes. Mol Cell. 2003 Nov;12(5):1165-72. PubMed PMID: 14636575. 2: Aravind L, Koonin EV. DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history. Nucleic Acids Res. 1999 Apr 1;27(7):1609-18. PubMed PMID: 10075991; PubMed Central PMCID: PMC148363. 3: Yue D, Maizels N, Weiner AM. CCA-adding enzymes and poly(A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA. 1996 Sep;2(9):895-908. PubMed PMID: 8809016; PubMed Central PMCID: PMC1369424. 4: Sakon J, Liao HH, Kanikula AM, Benning MM, Rayment I, Holden HM. Molecular structure of kanamycin nucleotidyltransferase determined to 3.0-A resolution. Biochemistry. 1993 Nov 16;32(45):11977-84. PubMed PMID: 8218273. 5: Holm L, Sander C. DNA polymerase beta belongs to an ancient nucleotidyltransferase superfamily. Trends Biochem Sci. 1995 Sep;20(9):345-7. PubMed PMID: 7482698. ----------------------------------- ----------------------------------- #4 c.1 Ancestry = 0.019 > d1r5ya_ c.1.20.1 (A:) Queosine tRNA-guanine transglycosylase {Zymomonas mobilis [TaxId: 542]} > d1iq8a1 c.1.20.1 (A:6-360) Archaeosine tRNA-guanine transglycosylase, N-terminal domain {Archaeon Pyrococcus horikoshii [TaxId: 53953]} 1: Brenk R, Meyer EA, Reuter K, Stubbs MT, Garcia GA, Diederich F, Klebe G. Crystallographic study of inhibitors of tRNA-guanine transglycosylase suggests a new structure-based pharmacophore for virtual screening. J Mol Biol. 2004 Apr 16;338(1):55-75. PubMed PMID: 15050823. 2: Romier C, Ficner R, Reuter K, Suck D. Purification, crystallization, and preliminary x-ray diffraction studies of tRNA-guanine transglycosylase from Zymomonas mobilis. Proteins. 1996 Apr;24(4):516-9. PubMed PMID: 8860000. 3: Romier C, Reuter K, Suck D, Ficner R. Crystal structure of tRNA-guanine transglycosylase: RNA modification by base exchange. EMBO J. 1996 Jun 3;15(11):2850-7. PubMed PMID: 8654383; PubMed Central PMCID: PMC450223. 4: Garcia GA, Koch KA, Chong S. tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure. J Mol Biol. 1993 May 20;231(2):489-97. PubMed PMID: 8323579. > d1vhna_ c.1.4.1 (A:) Putative flavin oxidoreducatase TM0096 {Thermotoga maritima [TaxId: 2336]} 1: Xing F, Martzen MR, Phizicky EM. A conserved family of Saccharomyces cerevisiae synthases effects dihydrouridine modification of tRNA. RNA. 2002 Mar;8(3):370-81. PubMed PMID: 12003496; PubMed Central PMCID: PMC1370258. 2: Bishop AC, Xu J, Johnson RC, Schimmel P, de Crcy-Lagard V. Identification of the tRNA-dihydrouridine synthase family. J Biol Chem. 2002 Jul 12;277(28):25090-5. Epub 2002 Apr 30. PubMed PMID: 11983710. ----------------------------------- ----------------------------------- #5 c.2 Ancestry = 0.025 > d1gpja2 c.2.1.7 (A:144-302) Glutamyl tRNA-reductase middle domain {Archaeon Methanopyrus kandleri [TaxId: 2320]} ***ASSOCIATED WITH TETRAPYROLE SYNTHESIS, NOT TRANSLATION*** 1: Michel G, Roszak AW, Sauv V, Maclean J, Matte A, Coggins JR, Cygler M, Lapthorn AJ. Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities. J Biol Chem. 2003 May 23;278(21):19463-72. Epub 2003 Mar 12. PubMed PMID: 12637497. 2: Benach J, Lee I, Edstrom W, Kuzin AP, Chiang Y, Acton TB, Montelione GT, Hunt JF. The 2.3-A crystal structure of the shikimate 5-dehydrogenase orthologue YdiB from Escherichia coli suggests a novel catalytic environment for an NAD-dependent dehydrogenase. J Biol Chem. 2003 May 23;278(21):19176-82. Epub 2003 Mar 6. PubMed PMID: 12624088. 3: Moser J, Schubert WD, Beier V, Bringemeier I, Jahn D, Heinz DW. V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. EMBO J. 2001 Dec 3;20(23):6583-90. PubMed PMID: 11726494; PubMed Central PMCID: PMC125327. 4: Hawkins AR, Lamb HK. The molecular biology of multidomain proteins. Selected examples. Eur J Biochem. 1995 Aug 15;232(1):7-18. Review. PubMed PMID: 7556173. ----------------------------------- ----------------------------------- #6 c.23 Ancestry = 0.031 > d1j5eb_ c.23.15.1 (B:) Ribosomal protein S2 {Thermus thermophilus [TaxId: 274]} > d1vi6a_ c.23.15.1 (A:) Ribosomal protein S2 {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} 1: Choi S, Jung CR, Kim JY, Im DS. PRMT3 inhibits ubiquitination of ribosomal protein S2 and together forms an active enzyme complex. Biochim Biophys Acta. 2008 Sep;1780(9):1062-9. Epub 2008 Jun 3. PubMed PMID: 18573314. 2: Pisarev AV, Kolupaeva VG, Yusupov MM, Hellen CU, Pestova TV. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J. 2008 Jun 4;27(11):1609-21. Epub 2008 May 8. PubMed PMID: 18464793; PubMed Central PMCID: PMC2426728. 3: Nelson J, McFerran NV, Pivato G, Chambers E, Doherty C, Steele D, Timson DJ. The 67 kDa laminin receptor: structure, function and role in disease. Biosci Rep. 2008 Feb;28(1):33-48. Review. PubMed PMID: 18269348. 4: Jamieson KV, Wu J, Hubbard SR, Meruelo D. Crystal structure of the human laminin receptor precursor. J Biol Chem. 2008 Feb 8;283(6):3002-5. Epub 2007 Dec 6. PubMed PMID: 18063583. 5: Yusupova G, Jenner L, Rees B, Moras D, Yusupov M. Structural basis for messenger RNA movement on the ribosome. Nature. 2006 Nov 16;444(7117):391-4. Epub 2006 Oct 18. PubMed PMID: 17051149. 6: Swiercz R, Person MD, Bedford MT. Ribosomal protein S2 is a substrate for mammalian PRMT3 (protein arginine methyltransferase 3). Biochem J. 2005 Feb 15;386(Pt 1):85-91. PubMed PMID: 15473865; PubMed Central PMCID: PMC1134769. 7: Kowalczyk P, Woszczynski M, Ostrowski J. Increased expression of ribosomal protein S2 in liver tumors, posthepactomized livers, and proliferating hepatocytes in vitro. Acta Biochim Pol. 2002;49(3):615-24. PubMed PMID: 12422231. 8: Moll I, Grill S, Grndling A, Blsi U. Effects of ribosomal proteins S1, S2 and the DeaD/CsdA DEAD-box helicase on translation of leaderless and canonical mRNAs in Escherichia coli. Mol Microbiol. 2002 Jun;44(5):1387-96. PubMed PMID: 12068815. 9: Loging WT, Reisman D. Elevated expression of ribosomal protein genes L37, RPP-1, and S2 in the presence of mutant p53. Cancer Epidemiol Biomarkers Prev. 1999 Nov;8(11):1011-6. PubMed PMID: 10566557. 10: Rieger R, Lasmzas CI, Weiss S. Role of the 37 kDa laminin receptor precursor in the life cycle of prions. Transfus Clin Biol. 1999 Feb;6(1):7-16. Review. PubMed PMID: 10188208. 11: Ardini E, Pesole G, Tagliabue E, Magnifico A, Castronovo V, Sobel ME, Colnaghi MI, Mnard S. The 67-kDa laminin receptor originated from a ribosomal protein that acquired a dual function during evolution. Mol Biol Evol. 1998 Aug;15(8):1017-25. PubMed PMID: 9718729. 12: An G, Bendiak DS, Mamelak LA, Friesen JD. Organization and nucleotide sequence of a new ribosomal operon in Escherichia coli containing the genes for ribosomal protein S2 and elongation factor Ts. Nucleic Acids Res. 1981 Aug 25;9(16):4163-72. PubMed PMID: 6272196; PubMed Central PMCID: PMC1058473. 13: Schwedler-Breitenreuter G, Lotti M, Stffler-Meilicke M, Stffler G. Localization of ribosomal protein S2 on the surface of the 30S subunit from Escherichia coli, using monoclonal antibodies. EMBO J. 1985 Aug;4(8):2109-12. PubMed PMID: 3905390; PubMed Central PMCID: PMC554469. 14: Chiao PJ, Shin DM, Sacks PG, Hong WK, Tainsky MA. Elevated expression of the ribosomal protein S2 gene in human tumors. Mol Carcinog. 1992;5(3):219-31. PubMed PMID: 1586449. ----------------------------------- ----------------------------------- #7 c.55 0.038 > d1ilya_ c.55.4.1 (A:) Ribosomal protein L18 (L18p) {Thermus thermophilus [TaxId: 274]} > d1jj2m_ c.55.4.1 (M:) Ribosomal protein L18 (L18p) {Archaeon Haloarcula marismortui [TaxId: 2238]} 1: Korepanov AP, Gongadze GM, Garber MB, Court DL, Bubunenko MG. Importance of the 5 S rRNA-binding ribosomal proteins for cell viability and translation in Escherichia coli. J Mol Biol. 2007 Mar 2;366(4):1199-208. Epub 2006 Dec 15. PubMed PMID: 17198710; PubMed Central PMCID: PMC1939977. 2: Turner CF, Moore PB. The solution structure of ribosomal protein L18 from Bacillus stearothermophilus. J Mol Biol. 2004 Jan 16;335(3):679-84. PubMed PMID: 14687565. 3: Woestenenk EA, Gongadze GM, Shcherbakov DV, Rak AV, Garber MB, Hrd T, Berglund H. The solution structure of ribosomal protein L18 from Thermus thermophilus reveals a conserved RNA-binding fold. Biochem J. 2002 May 1;363(Pt 3):553-61. PubMed PMID: 11964156; PubMed Central PMCID: PMC1222508. 4: Willumeit R, Diedrich G, Forthmann S, Beckmann J, May RP, Stuhrmann HB, Nierhaus KH. Mapping proteins of the 50S subunit from Escherichia coli ribosomes. Biochim Biophys Acta. 2001 Jul 30;1520(1):7-20. PubMed PMID: 11470155. 5: Nissen P, Hansen J, Ban N, Moore PB, Steitz TA. The structural basis of ribosome activity in peptide bond synthesis. Science. 2000 Aug 11;289(5481):920-30. PubMed PMID: 10937990. 6: Ban N, Nissen P, Hansen J, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science. 2000 Aug 11;289(5481):905-20. PubMed PMID: 10937989. 7: Bloemink MJ, Moore PB. Phosphorylation of ribosomal protein L18 is required for its folding and binding to 5S rRNA. Biochemistry. 1999 Oct 5;38(40):13385-90. PubMed PMID: 10529214. 8: Michael WM, Dreyfuss G. Distinct domains in ribosomal protein L5 mediate 5 S rRNA binding and nucleolar localization. J Biol Chem. 1996 May 10;271(19):11571-4. PubMed PMID: 8626719. > d1j5ek_ c.55.4.1 (K:) Ribosomal protein S11 {Thermus thermophilus [TaxId: 274]} 1: Robert F, Brakier-Gingras L. A functional interaction between ribosomal proteins S7 and S11 within the bacterial ribosome. J Biol Chem. 2003 Nov 7;278(45):44913-20. Epub 2003 Aug 22. PubMed PMID: 12937172. 2: Tallada VA, Daga RR, Palomeque C, Garzn A, Jimenez J. Genome-wide search of Schizosaccharomyces pombe genes causing overexpression-mediated cell cycle defects. Yeast. 2002 Sep 30;19(13):1139-51. PubMed PMID: 12237855. 3: Kamp R, Wittmann-Liebold B. Primary structure of protein S11 from Escherichia coli ribosomes. FEBS Lett. 1980 Nov 17;121(1):117-22. PubMed PMID: 7007074. 4: Baughman G, Nomura M. Localization of the target site for translational regulation of the L11 operon and direct evidence for translational coupling in Escherichia coli. Cell. 1983 Oct;34(3):979-88. PubMed PMID: 6354472. 5: Kimura M, Kimura J, Hatakeyama T. Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family. FEBS Lett. 1988 Nov 21;240(1-2):15-20. PubMed PMID: 3191988. 6: Markmann-Mulisch U, Subramanian AR. Nucleotide sequence of maize chloroplast rpS11 with conserved amino acid sequence between eukaryotes, bacteria and plastids. Biochem Int. 1988 Oct;17(4):655-64. PubMed PMID: 3149198. 7: Larkin JC, Thompson JR, Woolford JL Jr. Structure and expression of the Saccharomyces cerevisiae CRY1 gene: a highly conserved ribosomal protein gene. Mol Cell Biol. 1987 May;7(5):1764-75. PubMed PMID: 3037334; PubMed Central PMCID: PMC365278. 8: Powers T, Stern S, Changchien LM, Noller HF. Probing the assembly of the 3' major domain of 16 S rRNA. Interactions involving ribosomal proteins S2, S3, S10, S13 and S14. J Mol Biol. 1988 Jun 20;201(4):697-716. PubMed PMID: 2459390. 9: Stern S, Powers T, Changchien LM, Noller HF. Interaction of ribosomal proteins S5, S6, S11, S12, S18 and S21 with 16 S rRNA. J Mol Biol. 1988 Jun 20;201(4):683-95. PubMed PMID: 2459389. 10: Wiener L, Brimacombe R. Protein binding sites on Escherichia coli 16S RNA; RNA regions that are protected by proteins S7, S14 and S19 in the presence or absence of protein S9. Nucleic Acids Res. 1987 May 11;15(9):3653-70. PubMed PMID: 2438658; PubMed Central PMCID: PMC340774. 11: Ramagopal S. Subcellular distribution of ribosomal proteins in Dictyostelium discoideum. Biochem Cell Biol. 1990 May;68(5):838-45. PubMed PMID: 2400592. > d1yt3a3 c.55.3.5 (A:1-193) Ribonuclease D, catalytic domain {Escherichia coli [TaxId: 562]} 1: Ibrahim H, Wilusz J, Wilusz CJ. RNA recognition by 3'-to-5' exonucleases: the substrate perspective. Biochim Biophys Acta. 2008 Apr;1779(4):256-65. Epub 2007 Dec 3. Review. PubMed PMID: 18078842; PubMed Central PMCID: PMC2365504. 2: Zuo Y, Wang Y, Malhotra A. Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing. Structure. 2005 Jul;13(7):973-84. PubMed PMID: 16004870. 3: Shevelev IV, Hbscher U. The 3' 5' exonucleases. Nat Rev Mol Cell Biol. 2002 May;3(5):364-76. Review. PubMed PMID: 11988770. 4: Zuo Y, Deutscher MP. Exoribonuclease superfamilies: structural analysis and phylogenetic distribution. Nucleic Acids Res. 2001 Mar 1;29(5):1017-26. Review. PubMed PMID: 11222749; PubMed Central PMCID: PMC56904. 5: van Hoof A, Lennertz P, Parker R. Three conserved members of the RNase D family have unique and overlapping functions in the processing of 5S, 5.8S, U4, U5, RNase MRP and RNase P RNAs in yeast. EMBO J. 2000 Mar 15;19(6):1357-65. PubMed PMID: 10716935; PubMed Central PMCID: PMC305676. 6: Moser MJ, Holley WR, Chatterjee A, Mian IS. The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. Nucleic Acids Res. 1997 Dec 15;25(24):5110-8. PubMed PMID: 9396823; PubMed Central PMCID: PMC147149. 7: Mian IS. Comparative sequence analysis of ribonucleases HII, III, II PH and D. Nucleic Acids Res. 1997 Aug 15;25(16):3187-95. PubMed PMID: 9241229; PubMed Central PMCID: PMC146874. 8: Zhang JR, Deutscher MP. Escherichia coli RNase D: sequencing of the rnd structural gene and purification of the overexpressed protein. Nucleic Acids Res. 1988 Jul 25;16(14A):6265-78. PubMed PMID: 3041371; PubMed Central PMCID: PMC338294. 9: Hostomsky Z, Hudson GO, Rahmati S, Hostomska Z. RNase D, a reported new activity associated with HIV-1 reverse transcriptase, displays the same cleavage specificity as Escherichia coli RNase III. Nucleic Acids Res. 1992 Nov 11;20(21):5819-24. PubMed PMID: 1280810; PubMed Central PMCID: PMC334421. ----------------------------------- ----------------------------------- #8 b.40 Ancestry = 0.044 > d1bkba2 b.40.4.5 (A:75-139) C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) {Archaeon Pyrobaculum aerophilum [TaxId: 13773]} 1: Zanelli CF, Maragno AL, Gregio AP, Komili S, Pandolfi JR, Mestriner CA, Lustri WR, Valentini SR. eIF5A binds to translational machinery components and affects translation in yeast. Biochem Biophys Res Commun. 2006 Oct 6;348(4):1358-66. Epub 2006 Aug 7. PubMed PMID: 16914118. 2: Jao DL, Chen KY. Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex. J Cell Biochem. 2006 Feb 15;97(3):583-98. PubMed PMID: 16215987. 3: Theobald DL, Mitton-Fry RM, Wuttke DS. Nucleic acid recognition by OB-fold proteins. Annu Rev Biophys Biomol Struct. 2003;32:115-33. Epub 2003 Feb 18. Review. PubMed PMID: 12598368; PubMed Central PMCID: PMC1564333. 4: Peat TS, Newman J, Waldo GS, Berendzen J, Terwilliger TC. Structure of translation initiation factor 5A from Pyrobaculum aerophilum at 1.75 A resolution. Structure. 1998 Sep 15;6(9):1207-14. PubMed PMID: 9753699. 5: Kim KK, Hung LW, Yokota H, Kim R, Kim SH. Crystal structures of eukaryotic translation initiation factor 5A from Methanococcus jannaschii at 1.8 A resolution. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10419-24. PubMed PMID: 9724718; PubMed Central PMCID: PMC27909. > d1khia2 b.40.4.5 (A:103-173) C-terminal domain of eIF5a homologue (Hex1) {Filamentous fungi (Neurospora crassa) [TaxId: 5141]} ***ASSOCIATED WITH WORONIN BODY, NOT TRANSLATION*** 1: Curach NC, Te'o VS, Gibbs MD, Bergquist PL, Nevalainen KM. Isolation, characterization and expression of the hex1 gene from Trichoderma reesei. Gene. 2004 Apr 28;331:133-40. PubMed PMID: 15094199. 2: Yuan P, Jedd G, Kumaran D, Swaminathan S, Shio H, Hewitt D, Chua NH, Swaminathan K. A HEX-1 crystal lattice required for Woronin body function in Neurospora crassa. Nat Struct Biol. 2003 Apr;10(4):264-70. PubMed PMID: 12640443. 3: Tenney K, Hunt I, Sweigard J, Pounder JI, McClain C, Bowman EJ, Bowman BJ. Hex-1, a gene unique to filamentous fungi, encodes the major protein of the Woronin body and functions as a plug for septal pores. Fungal Genet Biol. 2000 Dec;31(3):205-17. PubMed PMID: 11273682. > d1x6oa2 b.40.4.5 (A:87-165) C-terminal domain of eukaryotic initiation translation factor 5a (eIF5a) {Leishmania infantum [TaxId: 5671]} 1: Zanelli CF, Maragno AL, Gregio AP, Komili S, Pandolfi JR, Mestriner CA, Lustri WR, Valentini SR. eIF5A binds to translational machinery components and affects translation in yeast. Biochem Biophys Res Commun. 2006 Oct 6;348(4):1358-66. Epub 2006 Aug 7. PubMed PMID: 16914118. 2: Jao DL, Chen KY. Tandem affinity purification revealed the hypusine-dependent binding of eukaryotic initiation factor 5A to the translating 80S ribosomal complex. J Cell Biochem. 2006 Feb 15;97(3):583-98. PubMed PMID: 16215987. 3: Theobald DL, Mitton-Fry RM, Wuttke DS. Nucleic acid recognition by OB-fold proteins. Annu Rev Biophys Biomol Struct. 2003;32:115-33. Epub 2003 Feb 18. Review. PubMed PMID: 12598368; PubMed Central PMCID: PMC1564333. > d1ueba2 b.40.4.5 (A:64-126) Elongation factor P middle and C-terminal domains {Thermus thermophilus HB8 [TaxId: 300852]} > d1ueba3 b.40.4.5 (A:127-184) Elongation factor P middle and C-terminal domains {Thermus thermophilus HB8 [TaxId: 300852]} 1: Swaney S, McCroskey M, Shinabarger D, Wang Z, Turner BA, Parker CN. Characterization of a high-throughput screening assay for inhibitors of elongation factor p and ribosomal peptidyl transferase activity. J Biomol Screen. 2006 Oct;11(7):736-42. Epub 2006 Aug 23. PubMed PMID: 16928980. 2: Nilsson J, Nissen P. Elongation factors on the ribosome. Curr Opin Struct Biol. 2005 Jun;15(3):349-54. Review. PubMed PMID: 15922593. 3: Hanawa-Suetsugu K, Sekine S, Sakai H, Hori-Takemoto C, Terada T, Unzai S, Tame JR, Kuramitsu S, Shirouzu M, Yokoyama S. Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9595-600. Epub 2004 Jun 21. PubMed PMID: 15210970; PubMed Central PMCID: PMC470720. 4: Andersen GR, Nissen P, Nyborg J. Elongation factors in protein biosynthesis. Trends Biochem Sci. 2003 Aug;28(8):434-41. Review. PubMed PMID: 12932732. 5: Aoki H, Dekany K, Adams SL, Ganoza MC. The gene encoding the elongation factor P protein is essential for viability and is required for protein synthesis. J Biol Chem. 1997 Dec 19;272(51):32254-9. PubMed PMID: 9405429. > d1b8aa1 b.40.4.1 (A:1-103) Aspartyl-tRNA synthetase (AspRS) {Archaeon Pyrococcus kodakaraensis [TaxId: 311400]} 1: Tumbula-Hansen D, Feng L, Toogood H, Stetter KO, Sll D. Evolutionary divergence of the archaeal aspartyl-tRNA synthetases into discriminating and nondiscriminating forms. J Biol Chem. 2002 Oct 4;277(40):37184-90. Epub 2002 Jul 30. PubMed PMID: 12149259. 2: Szymanski M, Deniziak MA, Barciszewski J. Aminoacyl-tRNA synthetases database. Nucleic Acids Res. 2001 Jan 1;29(1):288-90. PubMed PMID: 11125115; PubMed Central PMCID: PMC29805. 3: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 4: Schmitt E, Moulinier L, Fujiwara S, Imanaka T, Thierry JC, Moras D. Crystal structure of aspartyl-tRNA synthetase from Pyrococcus kodakaraensis KOD: archaeon specificity and catalytic mechanism of adenylate formation. EMBO J. 1998 Sep 1;17(17):5227-37. PubMed PMID: 9724658; PubMed Central PMCID: PMC1170850. 5: Cusack S. Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update. Biochimie. 1993;75(12):1077-81. Review. PubMed PMID: 8199242. 6: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. 7: Cusack S, Hrtlein M, Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 1991 Jul 11;19(13):3489-98. PubMed PMID: 1852601; PubMed Central PMCID: PMC328370. > d1l0wa1 b.40.4.1 (A:1-104) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-1 [TaxId: 274]} > d1n9wa1 b.40.4.1 (A:1-93) Aspartyl-tRNA synthetase (AspRS) {Thermus thermophilus, AspRS-2 [TaxId: 274]} 1: Chuawong P, Hendrickson TL. The nondiscriminating aspartyl-tRNA synthetase from Helicobacter pylori: anticodon-binding domain mutations that impact tRNA specificity and heterologous toxicity. Biochemistry. 2006 Jul 4;45(26):8079-87. PubMed PMID: 16800632; PubMed Central PMCID: PMC2654173. 2: Bonnefond L, Fender A, Rudinger-Thirion J, Gieg R, Florentz C, Sissler M. Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS. Biochemistry. 2005 Mar 29;44(12):4805-16. PubMed PMID: 15779907. 3: Ng JD, Sauter C, Lorber B, Kirkland N, Arnez J, Gieg R. Comparative analysis of space-grown and earth-grown crystals of an aminoacyl-tRNA synthetase: space-grown crystals are more useful for structural determination. Acta Crystallogr D Biol Crystallogr. 2002 Apr;58(Pt 4):645-52. Epub 2002 Mar 22. PubMed PMID: 11914489. 4: Moulinier L, Eiler S, Eriani G, Gangloff J, Thierry JC, Gabriel K, McClain WH, Moras D. The structure of an AspRS-tRNA(Asp) complex reveals a tRNA-dependent control mechanism. EMBO J. 2001 Sep 17;20(18):5290-301. PubMed PMID: 11566892; PubMed Central PMCID: PMC125622. 5: Charron C, Roy H, Lorber B, Kern D, Gieg R. Crystallization and preliminary X-ray diffraction data of the second and archaebacterial-type aspartyl-tRNA synthetase from Thermus thermophilus. Acta Crystallogr D Biol Crystallogr. 2001 Aug;57(Pt 8):1177-9. Epub 2001 Jul 23. PubMed PMID: 11468411. 6: Szymanski M, Deniziak MA, Barciszewski J. Aminoacyl-tRNA synthetases database. Nucleic Acids Res. 2001 Jan 1;29(1):288-90. PubMed PMID: 11125115; PubMed Central PMCID: PMC29805. 7: Briand C, Poterszman A, Eiler S, Webster G, Thierry J, Moras D. An intermediate step in the recognition of tRNA(Asp) by aspartyl-tRNA synthetase. J Mol Biol. 2000 Jun 16;299(4):1051-60. PubMed PMID: 10843857. 8: Becker HD, Roy H, Moulinier L, Mazauric MH, Keith G, Kern D. Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase. Biochemistry. 2000 Mar 28;39(12):3216-30. PubMed PMID: 10727213. 9: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 10: Eiler S, Dock-Bregeon A, Moulinier L, Thierry JC, Moras D. Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step. EMBO J. 1999 Nov 15;18(22):6532-41. PubMed PMID: 10562565; PubMed Central PMCID: PMC1171716. 11: Cusack S. Sequence, structure and evolutionary relationships between class 2 aminoacyl-tRNA synthetases: an update. Biochimie. 1993;75(12):1077-81. Review. PubMed PMID: 8199242. 12: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. 13: Cusack S, Hrtlein M, Leberman R. Sequence, structural and evolutionary relationships between class 2 aminoacyl-tRNA synthetases. Nucleic Acids Res. 1991 Jul 11;19(13):3489-98. PubMed PMID: 1852601; PubMed Central PMCID: PMC328370. > d1jjcb3 b.40.4.4 (B:39-151) Domain B2 of PheRS-beta, PheT {Thermus thermophilus [TaxId: 274]} > d1hr0w_ b.40.4.5 (W:) Translational initiation factor 1, IF1 {Escherichia coli [TaxId: 562]} 1: Croitoru V, Semrad K, Prenninger S, Rajkowitsch L, Vejen M, Laursen BS, Sperling-Petersen HU, Isaksson LA. RNA chaperone activity of translation initiation factor IF1. Biochimie. 2006 Dec;88(12):1875-82. Epub 2006 Aug 8. PubMed PMID: 16938378. 1: Goldgur Y, Mosyak L, Reshetnikova L, Ankilova V, Lavrik O, Khodyreva S, Safro M. The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. Structure. 1997 Jan 15;5(1):59-68. PubMed PMID: 9016717. 2: Lomakin IB, Kolupaeva VG, Marintchev A, Wagner G, Pestova TV. Position of eukaryotic initiation factor eIF1 on the 40S ribosomal subunit determined by directed hydroxyl radical probing. Genes Dev. 2003 Nov 15;17(22):2786-97. Epub 2003 Nov 4. PubMed PMID: 14600024; PubMed Central PMCID: PMC280627. 3: Carter AP, Clemons WM Jr, Brodersen DE, Morgan-Warren RJ, Hartsch T, Wimberly BT, Ramakrishnan V. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science. 2001 Jan 19;291(5503):498-501. PubMed PMID: 11228145. 4: Dahlquist KD, Puglisi JD. Interaction of translation initiation factor IF1 with the E. coli ribosomal A site. J Mol Biol. 2000 May 26;299(1):1-15. PubMed PMID: 10860719. 5: Sette M, van Tilborg P, Spurio R, Kaptein R, Paci M, Gualerzi CO, Boelens R. The structure of the translational initiation factor IF1 from E.coli contains an oligomer-binding motif. EMBO J. 1997 Mar 17;16(6):1436-43. PubMed PMID: 9135158; PubMed Central PMCID: PMC1169740. 6: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell. 1997 Jan 24;88(2):235-42. PubMed PMID: 9008164. > d1jt8a_ b.40.4.5 (A:) Archaeal initiation factor-1a, aIF1a {Archaeon Methanococcus jannaschii [TaxId: 2190]} 1: Li W, Hoffman DW. Structure and dynamics of translation initiation factor aIF-1A from the archaeon Methanococcus jannaschii determined by NMR spectroscopy. Protein Sci. 2001 Dec;10(12):2426-38. PubMed PMID: 11714910; PubMed Central PMCID: PMC2374032. 2: Pestova TV, Kolupaeva VG, Lomakin IB, Pilipenko EV, Shatsky IN, Agol VI, Hellen CU. Molecular mechanisms of translation initiation in eukaryotes. Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7029-36. Review. PubMed PMID: 11416183; PubMed Central PMCID: PMC34618. 3: Pestova TV, Hellen CU. The structure and function of initiation factors in eukaryotic protein synthesis. Cell Mol Life Sci. 2000 Apr;57(4):651-74. Review. PubMed PMID: 11130464. 4: Battiste JL, Pestova TV, Hellen CU, Wagner G. The eIF1A solution structure reveals a large RNA-binding surface important for scanning function. Mol Cell. 2000 Jan;5(1):109-19. PubMed PMID: 10678173. 5: Pestova TV, Borukhov SI, Hellen CU. Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons. Nature. 1998 Aug 27;394(6696):854-9. PubMed PMID: 9732867. 6: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell. 1997 Jan 24;88(2):235-42. PubMed PMID: 9008164. > d1pyba_ b.40.4.4 (A:) Structure-specific tRNA-binding protein TRBP111 {Aquifex aeolicus [TaxId: 63363]} 1: Kushiro T, Schimmel P. Trbp111 selectively binds a noncovalently assembled tRNA-like structure. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16631-5. Epub 2002 Dec 12. PubMed PMID: 12481025; PubMed Central PMCID: PMC139195. 2: Crepin T, Schmitt E, Blanquet S, Mechulam Y. Structure and function of the C-terminal domain of methionyl-tRNA synthetase. Biochemistry. 2002 Oct 29;41(43):13003-11. PubMed PMID: 12390027. 3: Nomanbhoy T, Morales AJ, Abraham AT, Vrtler CS, Gieg R, Schimmel P. Simultaneous binding of two proteins to opposite sides of a single transfer RNA. Nat Struct Biol. 2001 Apr;8(4):344-8. PubMed PMID: 11276256. 4: Swairjo MA, Morales AJ, Wang CC, Ortiz AR, Schimmel P. Crystal structure of trbp111: a structure-specific tRNA-binding protein. EMBO J. 2000 Dec 1;19(23):6287-98. PubMed PMID: 11101501; PubMed Central PMCID: PMC305853. 5: Morales AJ, Swairjo MA, Schimmel P. Structure-specific tRNA-binding protein from the extreme thermophile Aquifex aeolicus. EMBO J. 1999 Jun 15;18(12):3475-83. PubMed PMID: 10369686; PubMed Central PMCID: PMC1171426. > d1j5el_ b.40.4.5 (L:) Ribosomal protein S12 {Thermus thermophilus [TaxId: 274]} 1: Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH. Structures of the bacterial ribosome at 3.5 A resolution. Science. 2005 Nov 4;310(5749):827-34. PubMed PMID: 16272117. 2: Carr JF, Gregory ST, Dahlberg AE. Severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein S12 of Thermus thermophilus depends on the identity of highly conserved amino acid residues. J Bacteriol. 2005 May;187(10):3548-50. PubMed PMID: 15866943; PubMed Central PMCID: PMC1111998. 3: Vila-Sanjurjo A, Schuwirth BS, Hau CW, Cate JH. Structural basis for the control of translation initiation during stress. Nat Struct Mol Biol. 2004 Nov;11(11):1054-9. Epub 2004 Oct 24. Erratum in: Nat Struct Mol Biol. 2007 Apr;14(4):351. PubMed PMID: 15502846. 4: Chumpolkulwong N, Hori-Takemoto C, Hosaka T, Inaoka T, Kigawa T, Shirouzu M, Ochi K, Yokoyama S. Effects of Escherichia coli ribosomal protein S12 mutations on cell-free protein synthesis. Eur J Biochem. 2004 Mar;271(6):1127-34. PubMed PMID: 15009191. 5: Hosaka T, Tamehiro N, Chumpolkulwong N, Hori-Takemoto C, Shirouzu M, Yokoyama S, Ochi K. The novel mutation K87E in ribosomal protein S12 enhances protein synthesis activity during the late growth phase in Escherichia coli. Mol Genet Genomics. 2004 Apr;271(3):317-24. Epub 2004 Feb 14. PubMed PMID: 14966659. 6: Cukras AR, Southworth DR, Brunelle JL, Culver GM, Green R. Ribosomal proteins S12 and S13 function as control elements for translocation of the mRNA:tRNA complex. Mol Cell. 2003 Aug;12(2):321-8. PubMed PMID: 14536072. 7: Joseph S. After the ribosome structure: how does translocation work? RNA. 2003 Feb;9(2):160-4. Review. PubMed PMID: 12554856; PubMed Central PMCID: PMC1370379. 8: Stark H, Rodnina MV, Wieden HJ, Zemlin F, Wintermeyer W, van Heel M. Ribosome interactions of aminoacyl-tRNA and elongation factor Tu in the codon-recognition complex. Nat Struct Biol. 2002 Nov;9(11):849-54. PubMed PMID: 12379845. 9: Ramakrishnan V. Ribosome structure and the mechanism of translation. Cell. 2002 Feb 22;108(4):557-72. Review. PubMed PMID: 11909526. 10: Noller HF, Yusupov MM, Yusupova GZ, Baucom A, Cate JH. Translocation of tRNA during protein synthesis. FEBS Lett. 2002 Mar 6;514(1):11-6. Review. PubMed PMID: 11904173. 11: Spirin AS. Ribosome as a molecular machine. FEBS Lett. 2002 Mar 6;514(1):2-10. Review. PubMed PMID: 11904172. 12: Kornder JD. Streptomycin revisited: molecular action in the microbial cell. Med Hypotheses. 2002 Jan;58(1):34-46. PubMed PMID: 11863397. 13: Inaoka T, Kasai K, Ochi K. Construction of an in vivo nonsense readthrough assay system and functional analysis of ribosomal proteins S12, S4, and S5 in Bacillus subtilis. J Bacteriol. 2001 Sep;183(17):4958-63. PubMed PMID: 11489846; PubMed Central PMCID: PMC95369. 14: Suzuki T, Terasaki M, Takemoto-Hori C, Hanada T, Ueda T, Wada A, Watanabe K. Proteomic analysis of the mammalian mitochondrial ribosome. Identification of protein components in the 28 S small subunit. J Biol Chem. 2001 Aug 31;276(35):33181-95. Epub 2001 Jun 11. PubMed PMID: 11402041. 15: Gregory ST, Cate JH, Dahlberg AE. Streptomycin-resistant and streptomycin-dependent mutants of the extreme thermophile Thermus thermophilus. J Mol Biol. 2001 Jun 1;309(2):333-8. PubMed PMID: 11371156. 16: Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science. 2001 May 4;292(5518):897-902. PubMed PMID: 11340196. 17: Brodersen DE, Clemons WM Jr, Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell. 2000 Dec 22;103(7):1143-54. PubMed PMID: 11163189. 18: Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature. 2000 Sep 21;407(6802):340-8. PubMed PMID: 11014183. 19: Wimberly BT, Brodersen DE, Clemons WM Jr, Morgan-Warren RJ, Carter AP, Vonrhein C, Hartsch T, Ramakrishnan V. Structure of the 30S ribosomal subunit. Nature. 2000 Sep 21;407(6802):327-39. PubMed PMID: 11014182. > d1j5eq_ b.40.4.5 (Q:) Ribosomal protein S17 {Thermus thermophilus [TaxId: 274]} 1: Oura CA, Kinnaird J, Tait A, Shiels BR. Identification of a 40S Ribosomal protein (S17) that is differentially expressed between the macroschizont and piroplasm stages of Theileria annulata. Int J Parasitol. 2002 Jan;32(1):73-80. PubMed PMID: 11796124. 2: Simitsopoulou M, Avila H, Franceschi F. Ribosomal gene disruption in the extreme thermophile Thermus thermophilus HB8. Generation of a mutant lacking ribosomal protein S17. Eur J Biochem. 1999 Dec;266(2):524-32. PubMed PMID: 10561594. 3: Mueller F, Brimacombe R. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. II. The RNA-protein interaction data. J Mol Biol. 1997 Aug 29;271(4):545-65. PubMed PMID: 9281425. 4: Jaishree TN, Ramakrishnan V, White SW. Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy. Biochemistry. 1996 Mar 5;35(9):2845-53. PubMed PMID: 8608120. 5: Golden BL, Hoffman DW, Ramakrishnan V, White SW. Ribosomal protein S17: characterization of the three-dimensional structure by 1H and 15N NMR. Biochemistry. 1993 Nov 30;32(47):12812-20. PubMed PMID: 8251502. 6: Annesi F, Vespignani I, Amaldi F, Mariottini P. Xenopus laevis ribosomal protein S11: cloning and sequencing of the cDNA and primary structure of the protein. Biochem Biophys Res Commun. 1994 Sep 15;203(2):768-72. PubMed PMID: 8093055. 7: Yaguchi M, Wittmann HG. The primary structure of protein S17 from the small ribosomal subunit of Escherichia coli. FEBS Lett. 1978 Mar 1;87(1):37-40. PubMed PMID: 344065. 8: Herzog A, Yaguchi M, Cabezn T, Corchuelo MC, Petre J, Bollen A. A missense mutation in the gene coding for ribosomal protein S17 (rpsQ) leading to ribosomal assembly defectivity in Escherichia coli. Mol Gen Genet. 1979 Mar 9;171(1):15-22. PubMed PMID: 108517. > d1jj2a2 b.40.4.5 (A:1-90) N-terminal domain of ribosomal protein L2 {Archaeon Haloarcula marismortui [TaxId: 2238]} > d1rl2a2 b.40.4.5 (A:60-125) N-terminal domain of ribosomal protein L2 {Bacillus stearothermophilus [TaxId: 1422]} 1: Marty I, Meyer Y. cDNA nucleotide sequence and expression of a tobacco cytoplasmic ribosomal protein L2 gene. Nucleic Acids Res. 1992 Apr 11;20(7):1517-22. PubMed PMID: 1579444; PubMed Central PMCID: PMC312232. > d1ne3a_ b.40.4.5 (A:) Ribosomal protein S28e {Archaeon Methanobacterium thermoautotrophicum [TaxId: 145262]} 1: Wu B, Yee A, Pineda-Lucena A, Semesi A, Ramelot TA, Cort JR, Jung JW, Edwards A, Lee W, Kennedy M, Arrowsmith CH. Solution structure of ribosomal protein S28E from Methanobacterium thermoautotrophicum. Protein Sci. 2003 Dec;12(12):2831-7. PubMed PMID: 14627743; PubMed Central PMCID: PMC2366991. 2: Aramini JM, Huang YJ, Cort JR, Goldsmith-Fischman S, Xiao R, Shih LY, Ho CK, Liu J, Rost B, Honig B, Kennedy MA, Acton TB, Montelione GT. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii. Protein Sci. 2003 Dec;12(12):2823-30. PubMed PMID: 14627742; PubMed Central PMCID: PMC2366990. 3: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell. 1997 Jan 24;88(2):235-42. PubMed PMID: 9008164. > d2ahob2 b.40.4.5 (B:1-84) Eukaryotic initiation factor 2alpha, eIF2alpha, N-terminal domain {Sulfolobus solfataricus [TaxId: 2287]} 1: Yatime L, Schmitt E, Blanquet S, Mechulam Y. Structure-function relationships of the intact aIF2alpha subunit from the archaeon Pyrococcus abyssi. Biochemistry. 2005 Jun 21;44(24):8749-56. PubMed PMID: 15952781. 2: Dhaliwal S, Hoffman DW. The crystal structure of the N-terminal region of the alpha subunit of translation initiation factor 2 (eIF2alpha) from Saccharomyces cerevisiae provides a view of the loop containing serine 51, the target of the eIF2alpha-specific kinases. J Mol Biol. 2003 Nov 21;334(2):187-95. PubMed PMID: 14607111. 3: Ermolenko DN, Makhatadze GI. Bacterial cold-shock proteins. Cell Mol Life Sci. 2002 Nov;59(11):1902-13. Review. PubMed PMID: 12530521. 4: Nonato MC, Widom J, Clardy J. Crystal structure of the N-terminal segment of human eukaryotic translation initiation factor 2alpha. J Biol Chem. 2002 May 10;277(19):17057-61. Epub 2002 Feb 21. PubMed PMID: 11859078. 5: Bycroft M, Hubbard TJ, Proctor M, Freund SM, Murzin AG. The solution structure of the S1 RNA binding domain: a member of an ancient nucleic acid-binding fold. Cell. 1997 Jan 24;88(2):235-42. PubMed PMID: 9008164. 6: Pain VM. Initiation of protein synthesis in eukaryotic cells. Eur J Biochem. 1996 Mar 15;236(3):747-71. Review. PubMed PMID: 8665893. ----------------------------------- ----------------------------------- #9 c.66 Ancestry = 0.050 > d2b3ta1 c.66.1.30 (A:2-275) N5-glutamine methyltransferase, HemK {Escherichia coli [TaxId: 562]} > d1im8a_ c.66.1.14 (A:) Hypothetical protein HI0319 (YecO) {Haemophilus influenzae [TaxId: 727]} > d1i9ga_ c.66.1.13 (A:) Probable methyltransferase Rv2118c {Mycobacterium tuberculosis [TaxId: 1773]} > d1o54a_ c.66.1.13 (A:) Hypothetical protein TM0748 {Thermotoga maritima [TaxId: 2336]} > d1yzha1 c.66.1.53 (A:8-211) tRNA (guanine-N(7)-)-methyltransferase TrmB {Streptococcus pneumoniae [TaxId: 1313]} 1: Schubert HL, Blumenthal RM, Cheng X. Many paths to methyltransfer: a chronicle of convergence. Trends Biochem Sci. 2003 Jun;28(6):329-35. Review. PubMed PMID: 12826405; PubMed Central PMCID: PMC2758044. 2: Martin JL, McMillan FM. SAM (dependent) I AM: the S-adenosylmethionine-dependent methyltransferase fold. Curr Opin Struct Biol. 2002 Dec;12(6):783-93. Review. Erratum in: Curr Opin Struct Biol. 2003 Feb;13(1):142. PubMed PMID: 12504684. > d1yb2a1 c.66.1.13 (A:6-255) Hypothetical protein Ta0852 {Thermoplasma acidophilum [TaxId: 2303]} > d1g8aa_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Pyrococcus horikoshii [TaxId: 53953]} > d1nt2a_ c.66.1.3 (A:) Fibrillarin homologue {Archaeon Archaeoglobus fulgidus [TaxId: 2234]} --- first 10 0f 172 --- 1: Bai F, Li Y, Xu H, Xia H, Yin T, Yao H, Zhang L, Zhang X, Bai Y, Jin S, Qiao M. Identification and functional characterization of pfm, a novel gene involved in swimming motility of Pseudomonas aeruginosa. Gene. 2007 Oct 15;401(1-2):19-27. Epub 2007 Jul 10. PubMed PMID: 17714889. 2: Sergiev PV, Bogdanov AA, Dontsova OA. Ribosomal RNA guanine-(N2)-methyltransferases and their targets. Nucleic Acids Res. 2007;35(7):2295-301. Epub 2007 Mar 27. Review. PubMed PMID: 17389639; PubMed Central PMCID: PMC1874633. 3: Tucci S, Martin W. A novel prokaryotic trans-2-enoyl-CoA reductase from the spirochete Treponema denticola. FEBS Lett. 2007 Apr 17;581(8):1561-6. Epub 2007 Mar 15. PubMed PMID: 17382934. 4: Fleetwood DJ, Scott B, Lane GA, Tanaka A, Johnson RD. A complex ergovaline gene cluster in epichloe endophytes of grasses. Appl Environ Microbiol. 2007 Apr;73(8):2571-9. Epub 2007 Feb 16. PubMed PMID: 17308187; PubMed Central PMCID: PMC1855613. 5: Hausmann S, Ramirez A, Schneider S, Schwer B, Shuman S. Biochemical and genetic analysis of RNA cap guanine-N2 methyltransferases from Giardia lamblia and Schizosaccharomyces pombe. Nucleic Acids Res. 2007;35(5):1411-20. Epub 2007 Feb 6. PubMed PMID: 17284461; PubMed Central PMCID: PMC1865056. 6: Okamoto S, Tamaru A, Nakajima C, Nishimura K, Tanaka Y, Tokuyama S, Suzuki Y, Ochi K. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol Microbiol. 2007 Feb;63(4):1096-106. PubMed PMID: 17238915. 7: Blindauer CA, Razi MT, Campopiano DJ, Sadler PJ. Histidine ligands in bacterial metallothionein enhance cluster stability. J Biol Inorg Chem. 2007 Mar;12(3):393-405. Epub 2007 Jan 3. PubMed PMID: 17203314. 8: Lesnyak DV, Osipiuk J, Skarina T, Sergiev PV, Bogdanov AA, Edwards A, Savchenko A, Joachimiak A, Dontsova OA. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J Biol Chem. 2007 Feb 23;282(8):5880-7. Epub 2006 Dec 21. PubMed PMID: 17189261. 9: Khalimonchuk O, Ott M, Funes S, Ostermann K, Rdel G, Herrmann JM. Sequential processing of a mitochondrial tandem protein: insights into protein import in Schizosaccharomyces pombe. Eukaryot Cell. 2006 Jul;5(7):997-1006. PubMed PMID: 16835444; PubMed Central PMCID: PMC1489288. 10: McNally DJ, Hui JP, Aubry AJ, Mui KK, Guerry P, Brisson JR, Logan SM, Soo EC. Functional characterization of the flagellar glycosylation locus in Campylobacter jejuni 81-176 using a focused metabolomics approach. J Biol Chem. 2006 Jul 7;281(27):18489-98. Epub 2006 May 9. PubMed PMID: 16684771. ----------------------------------- ----------------------------------- #10 c.26 0.057 > d1irxa2 c.26.1.1 (A:3-319) Class I lysyl-tRNA synthetase {Archaeon Pyrococcus horikoshii [TaxId: 53953]} 1: O'Donoghue P, Luthey-Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev. 2003 Dec;67(4):550-73. Review. PubMed PMID: 14665676; PubMed Central PMCID: PMC309052. 2: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 3: Ambrogelly A, Korencic D, Ibba M. Functional annotation of class I lysyl-tRNA synthetase phylogeny indicates a limited role for gene transfer. J Bacteriol. 2002 Aug;184(16):4594-600. PubMed PMID: 12142429; PubMed Central PMCID: PMC135231. 4: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 5: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 6: Woese CR, Olsen GJ, Ibba M, Soll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 7: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 8: Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W, Lin W, Woese CR, Sll D. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science. 1997 Nov 7;278(5340):1119-22. PubMed PMID: 9353192. 9: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 10: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 11: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 12: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1gtra2 c.26.1.1 (A:8-338) Glutaminyl-tRNA synthetase (GlnRS) {Escherichia coli [TaxId: 562]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 3: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 4: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 5: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 6: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 7: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 8: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 9: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1u0bb2 c.26.1.1 (B:1-315) Cysteinyl-tRNA synthetase (CysRS) {Escherichia coli [TaxId: 562]} 1: O'Donoghue P, Luthey-Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev. 2003 Dec;67(4):550-73. Review. PubMed PMID: 14665676; PubMed Central PMCID: PMC309052. 2: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 3: Newberry KJ, Hou YM, Perona JJ. Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase. EMBO J. 2002 Jun 3;21(11):2778-87. PubMed PMID: 12032090; PubMed Central PMCID: PMC126036. 4: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 5: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 6: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 7: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 8: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 9: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 10: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 11: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1ffya3 c.26.1.1 (A:1-200,A:395-644) Isoleucyl-tRNA synthetase (IleRS) {Staphylococcus aureus [TaxId: 1280]} > d1ilea3 c.26.1.1 (A:1-197,A:387-641) Isoleucyl-tRNA synthetase (IleRS) {Thermus thermophilus [TaxId: 274]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 3: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 4: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 5: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 6: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 7: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 8: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 9: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1iq0a2 c.26.1.1 (A:97-466) Arginyl-tRNA synthetase (ArgRS) {Thermus thermophilus [TaxId: 274]} 1: O'Donoghue P, Luthey-Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev. 2003 Dec;67(4):550-73. Review. PubMed PMID: 14665676; PubMed Central PMCID: PMC309052. 2: Sekine S, Shimada A, Nureki O, Cavarelli J, Moras D, Vassylyev DG, Yokoyama S. Crucial role of the high-loop lysine for the catalytic activity of arginyl-tRNA synthetase. J Biol Chem. 2001 Feb 9;276(6):3723-6. Epub 2000 Dec 5. PubMed PMID: 11106639. 3: Zhou M, Wang ED, Campbell RL, Wang YL, Lin SX. Crystallization and preliminary X-ray diffraction analysis of arginyl-tRNA synthetase from Escherichia coli. Protein Sci. 1997 Dec;6(12):2636-8. PubMed PMID: 9416614; PubMed Central PMCID: PMC2143609. > d1ivsa4 c.26.1.1 (A:1-189,A:343-578) Valyl-tRNA synthetase (ValRS) {Thermus thermophilus [TaxId: 274]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 3: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 4: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 5: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 6: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 7: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 8: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 9: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1h3na3 c.26.1.1 (A:1-225,A:418-686) Leucyl-tRNA synthetase (LeuRS) {Thermus thermophilus [TaxId: 274]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Gouda M, Yokogawa T, Asahara H, Nishikawa K. Leucyl-tRNA synthetase from the extreme thermophile Aquifex aeolicus has a heterodimeric quaternary structure. FEBS Lett. 2002 May 8;518(1-3):139-43. PubMed PMID: 11997034. 3: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 4: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 5: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 6: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 7: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 8: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 9: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 10: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1h3fa1 c.26.1.1 (A:5-347) Tyrosyl-tRNA synthetase (TyrRS) {Thermus thermophilus [TaxId: 274]} > d1j1ua_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Archaeon Methanococcus jannaschii [TaxId: 2190]} > d1jila_ c.26.1.1 (A:) Tyrosyl-tRNA synthetase (TyrRS) {Staphylococcus aureus [TaxId: 1280]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 3: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 4: Beuning PJ, Musier-Forsyth K. Transfer RNA recognition by aminoacyl-tRNA synthetases. Biopolymers. 1999;52(1):1-28. Review. PubMed PMID: 10737860. 5: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 6: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 7: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 8: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 9: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1i6la_ c.26.1.1 (A:) Tryptophanyl-tRNA synthetase (TrpRS) {Bacillus stearothermophilus [TaxId: 1422]} 1: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 2: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 3: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 4: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 5: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 6: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 7: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 8: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 9: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1j09a2 c.26.1.1 (A:1-305) Glutamyl-tRNA synthetase (GluRS) {Thermus thermophilus [TaxId: 274]} > d1nzja_ c.26.1.1 (A:) Glutamyl-Q tRNA-Asp synthetase YadB {Escherichia coli [TaxId: 562]} 1: Sekine S, Nureki O, Dubois DY, Bernier S, Chnevert R, Lapointe J, Vassylyev DG, Yokoyama S. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J. 2003 Feb 3;22(3):676-88. PubMed PMID: 12554668; PubMed Central PMCID: PMC140737. 2: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 3: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 4: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 5: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 6: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 7: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 8: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 9: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 10: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1pfva2 c.26.1.1 (A:4-140,A:176-388) Methionyl-tRNA synthetase (MetRS) {Escherichia coli [TaxId: 562]} > d1rqga2 c.26.1.1 (A:1-138,A:174-396) Methionyl-tRNA synthetase (MetRS) {Pyrococcus abyssi [TaxId: 29292]} > d2d5ba2 c.26.1.1 (A:1-348) Methionyl-tRNA synthetase (MetRS) {Thermus thermophilus [TaxId: 274]} 1: O'Donoghue P, Luthey-Schulten Z. On the evolution of structure in aminoacyl-tRNA synthetases. Microbiol Mol Biol Rev. 2003 Dec;67(4):550-73. Review. PubMed PMID: 14665676; PubMed Central PMCID: PMC309052. 2: Francklyn C, Perona JJ, Puetz J, Hou YM. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. RNA. 2002 Nov;8(11):1363-72. Review. PubMed PMID: 12458790; PubMed Central PMCID: PMC1370343. 3: Crepin T, Schmitt E, Blanquet S, Mechulam Y. Structure and function of the C-terminal domain of methionyl-tRNA synthetase. Biochemistry. 2002 Oct 29;41(43):13003-11. PubMed PMID: 12390027. 4: Alexander RW, Schimmel P. Domain-domain communication in aminoacyl-tRNA synthetases. Prog Nucleic Acid Res Mol Biol. 2001;69:317-49. Review. PubMed PMID: 11550797. 5: Szymanski M, Deniziak M, Barciszewski J. The new aspects of aminoacyl-tRNA synthetases. Acta Biochim Pol. 2000;47(3):821-34. Review. PubMed PMID: 11310981. 6: Woese CR, Olsen GJ, Ibba M, Sll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol Mol Biol Rev. 2000 Mar;64(1):202-36. Review. PubMed PMID: 10704480; PubMed Central PMCID: PMC98992. 7: Wolf YI, Aravind L, Grishin NV, Koonin EV. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 1999 Aug;9(8):689-710. PubMed PMID: 10447505. 8: Delarue M, Moras D. The aminoacyl-tRNA synthetase family: modules at work. Bioessays. 1993 Oct;15(10):675-87. Review. PubMed PMID: 8274143. 9: Nagel GM, Doolittle RF. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J Mol Evol. 1995 May;40(5):487-98. PubMed PMID: 7783224. 10: Lands C, Perona JJ, Brunie S, Rould MA, Zelwer C, Steitz TA, Risler JL. A structure-based multiple sequence alignment of all class I aminoacyl-tRNA synthetases. Biochimie. 1995;77(3):194-203. PubMed PMID: 7647112. 11: Eriani G, Delarue M, Poch O, Gangloff J, Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 1990 Sep 13;347(6289):203-6. PubMed PMID: 2203971. > d1ni5a1 c.26.2.5 (A:0-226) tRNA-Ile-lysidine synthetase, TilS, N-terminal domain {Escherichia coli [TaxId: 562]} > d1wy5a1 c.26.2.5 (A:1-216) TilS-like protein Aq_1887 {Aquifex aeolicus [TaxId: 63363]} 1: Aravind L, Anantharaman V, Koonin EV. Monophyly of class I aminoacyl tRNA synthetase, USPA, ETFP, photolyase, and PP-ATPase nucleotide-binding domains: implications for protein evolution in the RNA. Proteins. 2002 Jul 1;48(1):1-14. PubMed PMID: 12012333. 2: Bork P, Koonin EV. A P-loop-like motif in a widespread ATP pyrophosphatase domain: implications for the evolution of sequence motifs and enzyme activity. Proteins. 1994 Dec;20(4):347-55. PubMed PMID: 7731953.