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. 2013 Jan 18;9:1–12. doi: 10.2142/biophysics.9.1

Table 1.

Functional classification of ATP-binding proteins

ATP hydrolysis, Pi is released (energy extration reaction)
  Protein Name Family PDB ID chain resol Uniprot ID

  vacuolar protein sorting-associating protein 4B AAA ATPase family 2zan A 3.00 VPS4B_MOUSE
  N-ethylmaleide sensitive factor AAA ATPase family 1nsf A 1.90 NSF_CRIGR
  FbpC nucleotide-binding domain ABC transporter domain 3fvq B 1.90 FBPC_NEIG1
  histidine permease ABC transporter superfamily 1b0u A 1.50 HISP_SALTY
  maltose/maltodextrin transport ATP-binding protein MalK ABC transporter superfamily 1q12 A 2.60 MALK_ECOLI
  ATP-binding cassette sub-family B meber 6 ABCB family 3nh9 A 2.10 ABCB6_HUMAN
  alpha actin 1 actin family 2fxu A 1.35 ACTS_RABIT
  actin-related protein 2 actin family 1tyq B 2.55 ARP3_BOVIN
  arsenical Pump-driving ATPase arsA ATPase family 1ii0 B 2.40 ARSA1_ECOLI
  ATP synthase subunit alpha ATPase alpha/beta chains family 2r9v A 2.10 ATPA_THEMA
  v-type ATP synthase beta chain ATPase alpha/beta chains family 3b2q A 2.10 VATB_METMA
  biotin carboxylase biotin carboxylation domain 1dv2 A 2.50 ACCC_ECOLI
  sarcoplasmic/endoplasmic reticulumn calcium ATPase 1 cation transport ATPase (P-type) family 3ar4 A 2.15 AT2A1_RABIT
  GroEL chaperonin (HSP60) family 1kp8 A 2.00 CH60_ECOLI
  heat shock locus U (HslU) clpX chaperone family 1do0 A 3.00 HSLU_ECOLI
  DNA mismatch repair protein Mlh1 DNA mismatch repair mutL/hexB family 3na3 A 2.50 MLH1_HUMAN
  DNA mismatch repair protein MutS DNA mismatch repair mutS family 1w7a A 2.27 MUTS_ECOLI
  PurL, Formylglycinamide ribonucleotide amidotransferase FGAMS family 2hs0 A 2.52 PURL_THEMA
  Gar synthetase (PurD) GARS family 2yw2 A 1.80 PUR2_AQUAE
  aspartyl/glutamyl-tRNA amidotransferase subunit B gatB/gatE family 3h0r H 3.00 GATB_AQUAE
  70kDa heat shock cognate protein heat shock protein 70 family 1kax A 1.70 HSP7C_BOVIN
  PcrA DNA helicase helicase family 1qhh B 2.50 PCRA_BACST
  nitrogenase iron protein 1 nifH/bchL/chlL family 2c8v A 2.50 NIH1_AZOVI
  cell division inhibitor MinD parA family 3q9l A 2.34 MIND_ECOLI
  bacterial chromosome segregation protein SoJ ParAB family 2bek A 1.80 Q72H90_THET2
  5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5′-monophosphate synthetase phosphohexose mutase family 2r7l A 2.10 PURP_METJA
  phosphoribosylaminoimidazole carboxylase ATPase subunit purK/purT family 3eth A 1.60 PURK_ECOLI
  glycinamide ribonucleotide transformylase (purT) purK/purT family 1kj9 B 1.60 PURT_ECOLI
  Holliday junction DNA helicase RuvB ruvB family 1j7k A 1.80 RUVB_THEMA
  phoshpribosylamidoimidazole-succinocarboxamide synthase SAICAR synthetase family 1obd A 1.40 PUR7_YEAST
  translocase SecA subunit secA family 2fsg B 2.20 SECA_ECOLI
  larget T antigen helicase domain SF3 helicase domain 1svm C 1.94 LT_SV40
  Psp operon transcriptional activator (PspF) sigma-54 factor interaction domain 2c96 A 1.80 PSPF_ECOLI
  Rad50 ABC-ATPase N-terminal domain SMC family 1f2u A 1.60 RAD50_PYRFU
  sulfiredoxin sulfiredoxin family 3cyi A 1.80 SRXN1_HUMAN
  NTPase P4 (molecular motor) superfamily 4 helicase motif 2vhq A 2.15 Q94M05_9VIRU
  transglutaminase 2 Transglutaminase family 3ly6 A 3.14 TGM2_HUMAN
  EcoR124I restriction enzyme HSDR subunit typeII restriction enzyme 2w00 B 2.60 Q304R3_ECOLX
  UvrABC component UvrB uvrB family 1d9z A 3.15 UVRB_BACCA
  twitching motility protein PilT not classified 2eww A 3.20 O66950_AQUAE
  transcriptional regulatory protein ZraR not classified 1ojl E 3.00 ZRAR_SALTY
  myosin II heavy chain not classified 1fmw A 2.15 MYS2_DICDI
  dethiobiotin synthetase not classified 1a82 A 1.80 BIOD_ECOLI

ATP hydrolysis, Pi is transferred (phosphprylation)
  Protein Name Family PDB ID chain resol Uniprot ID

  isocitrate dehydrogenase kinase/phosphatase (AceK) AceK family 3eps A 2.80 ACEK_ECO57
  cAMP-dependent protein kinase AGC Ser/Thr protein kinase family 3fjq E 1.60 KAPCA_MOUSE
  protein kinase C iota type AGC Ser/Thr protein kinase family: PKC subfamily 3a8w B 2.10 KPCI_HUMAN
  G protein coupled receptor kinase 1 (crystals of 6 different states) AGC Ser/Thr protein kinsae family: GRK kinase family 3c4w B 2.70 RK_BOVIN
  myosin heavy chain kinase A alpha-type protein kinase family 3lmi B 2.20 MHCKA_DICDI
  Isopentenyl phosphate kinase Amino acid kinase family 3ll5 C 1.99 Q9HLX1_THEAC
  anti-sigma F factor anti-sigma-factor family 1tid A 2.50 SP2AB_BACST
  ribokinase carbohydrate kinase pfkB family 3ikh A 1.88 A6T989_KLEP7
  casein kinase-1 CK1 Ser/Thr protein kinase family 1csn A 2.00 CKI1_SCHPO
  dephospho-CoA kinase coaE family 1jjv A 2.00 COAE_HAEIN
  mevalonate kinase GHMP kinase family 1kvk A 2.40 KIME_RAT
  gluconate kinase gluconokinase gntK/gntV family 1ko5 A 2.28 GNTK_ECOLI
  Inositol 1,4,5-triphosphate 3-kinase B inositol phosphokinase (IPK) family 2aqx A 2.50 IP3KB_RAT
  KaiC kaiC family 2gbl A 2.80 KAIC_SYNP7
  l-seryl-tRNA kinase L-seryl-tRNA(Sec) kinase family 3am1 A 2.40 PSTK_METJA
  NAD kinase NAD kinase family 1z0s A 1.70 PPNK_ARCFU
  nucleotide diphosphate kinase NDK family 1wkl B 2.20 NDK_THET8
  pyruvate dehydrogenase kinase isoform 2 PDK/BCKDK protein kinase family 2bu2 A 2.40 PDK2_HUMAN
  phosphoenolpyruvate carboxykinase phosphoenolpyruvate carboxykinase family 2olr A 1.60 PPCK_ECOLI
  phosphofruktokinase phosphofructokinase family 3o8l A 3.20 K6PF_RABIT
  phosphoglycerate kinase phosphoglycerate kinase family 1vjd A 1.90 PGK1_PIG
  phosphatidylinositol 3-kinase catalytic subunit PI3/PI4-kinase family 1e8x A 2.20 PK3CG_PIG
  polyhosphate kinase polyphosphate kinase family 1xdp A 2.50 PPK_ECOLI
  Pantothenate kinase prokaryotic pantothenate kinase family 2zsf A 2.80 COAA_MYCTU
  cell division protein kinse 2 protein kinase superfamily 2cch A 1.70 CDK2_HUMAN
  pyridoxine kinase pyridoxine kinase family 2ddo A 2.60 PDXK_ECOLI
  pyruvate kinase pyruvate kinase family 1a49 A 2.10 KPYM_RABIT
  Rio1 serine kinase RIO-type Ser/Thr kinase family 1zp9 A 2.00 RIO1_ARCFU
  Rio2 serine kinase RIO-type Ser/Thr kinase family 1zao A 1.84 RIO2_ARCFU
  mitotic checkpoint serine/threonin-protein kinase Bub1 Ser/Thr protein kinase family 3e7e A 2.31 BUB1_HUMAN
  SR protein kinase Ser/Thr protein kinase family 1q97 A 2.30 SKY1_YEAST
  shikimate kinase shikimate kinase family 2iyw A 1.85 AROK_MYCTU
  Tao2 kinase domain STE20 subfamily 1u5r A 2.10 TAOK2_RAT
  thymidylate kinase thymidylate kinase family 1e2q A 1.70 KTHY_HUMAN
  thiazole kinase Thz kinase family 1esq C 2.50 THIM_BACSU
  MET receptor tyrosine kinase Tyr protein kinase family 3dkc A 1.52 A1L467_HUMAN
  phosphofruktokinase not classified 3f5m B 2.70 O15648_9TRYP
  D-alanine-D-alanine ligase not classified 2zdq A 2.30 Q5SHZ3_THET8
  chloramphenicol phosphotransferase not classified 1qhx A 2.50 CPT_STRVL
  aminoglycoside phosphotransferase not classified 3hav B 2.45 Q9EVD7_ENTFC
  Thiamine monophosphate kinase not classified 3c9r A 2.30 O67883_AQUAE
  UMP kinase not classified 2jjx A 2.82 Q81S73_BACAN

ATP hydrolysis, PPi is released (energy extration reaction)
  Protein Name Family PDB ID chain resol Uniprot ID

  adenylate cyclase type 5 adenylyl cyclase class-4/guanylyl cyclase family 3c16 A 2.87 ADCY5_CANFA
  argininosuccinate synthetase argininosuccinate synthase family 1kp3 A 2.00 ASSY_ECOLI
  beta-lactam synthetase asparagine synthetase family 1mb9 B 2.11 BLS_STRCL
  Acyl-coenzyme A synthetase Acsm2A ATP-dependent AMP-binding enzyme 3c5e A 1.60 ACS2A_HUMAN
  D-alanine-polyphosphoribitol ligase subunit 1 ATP-dependent AMP-binding enzyme family 3fce A 1.90 DLTA_BACCR
  DNA ligase from bacteriophage T7 ATP-dependent DNA ligase family 1a0i A 2.60 DNLI_BPT7
  tryptophan-tRNA synthetase class-I aminoacyl-tRNA synthetase familiy 1mau A 2.15 SYW_BACST
  glutamyl-tRNA synthetase class-I aminoacyl-tRNA synthetase familiy 1j09 A 1.80 SYE_THET8
  glutaminyl-tRNA synthetase class-I aminoacyl-tRNA synthetase family 1gtr A 2.50 SYQ_ECOLI
  tyrosine-tRNA synthetase class-I aminoacyl-tRNA synthetase family 1h3e A 2.90 SYY_THETH
  tryptophanyl-tRNA synthetase class-I aminoacyl-tRNA synthetase family 2qui A 2.40 SYWC_HUMAN
  histidyl-tRNA synthetase class-II aminoacyl-tRNA synthetase familiy 1kmn C 2.80 SYH_ECOLI
  prolyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 2i4o A 2.40 SYP_RHOPA
  Class II AARS homologue (bll0957) class-II aminoacyl-tRNA synthetase family 3mey A 2.50 Q89VT8_BRAJA
  Lysyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 3bju A 2.31 SYK_HUMAN
  glycyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 2zt7 A 2.70 SYG_HUMAN
  pyrrolysyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 2q7g A 1.90 PYLS_METMA
  aspartyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 3nem B 1.89 SYD_PYRKO
  Threonyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 1nyr A 2.80 SYT_STAAW
  alanyl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 1yfr A 2.15 SYA_AQUAE
  serryl-tRNA synthetase class-II aminoacyl-tRNA synthetase family 3lss B 1.95 Q384V4_9TRYP
  tRNA-lysidine synthase tRNA(Ile)-lysidine synthase family 2e89 A 2.50 TILS_AQUAE
  prolyl-tRNA synthetase not classified 2j3m B 2.30 Q831W7_ENTFA
  serryl-tRNA synthetase not classified 2cja B 2.20 Q46AN5_METBA
  NH3-dependent NAD+ synthetase NAD synthetase family 1xng B 1.70 NADE_HELPY
  bacteriophage phi 6 RNA dependent RNA polymerase Polymerase family 1hi1 A 3.00 RDRP_BPPH6
  tRNA CCA-pyrophosphorylase tRNA nucleotidyltransferase/poly(A) polymerase family 3h39 B 2.85 Q9WZH4_THEMA
  polyA polymerase tRNA nucleotidyltransferase/poly(A) polymerase family 3aqn A 3.30 C9QS13_ECOD1
  RNA editing ligase Mp52 not classified 1xdn A 1.20 RLGM1_TRYBB

ATP hydrolysis, PPi is released and AMP is transferred (adenylation)
  Protein Name Family PDB ID chain resol Uniprot ID

  nicotinamide mononucleotide (NMN) adenylyltransferase archaeal NMN adenylyltransferase family 1f9a A 2.00 NADM_METJA
  phosphopantetheine adenylyltransferase bacterial coaD family 1gn8 A 1.83 COAD_ECOLI
  glucose-1-phosphate adenylyltransferase small bacterial/plant glucose-1-phosphate 1yp3 C 2.60 GLGS_SOLTU
  subunit adenylyltransferase family
  DNA polymerase IV DNA polymerase type-Y family 3m9o B 2.00 DPO42_SULSO
  adenylyltransferase ThiF hesA/moeB/thiF family 1zfn A 2.75 THIF_ECOLI
  lipoate-protein ligase A lplA family 2aru A 2.50 LPLA_THEAC
  nicotinate-nucleotide adenylyltransferase nadD family 1yun A 2.00 NADD_PSEAE
  pantoate-beta-alanine ligase pantothenate synthetase family 2a84 A 1.55 PANC_MYCTU
  polyA polymerase poly(A) polymerase family 2q66 A 1.80 PAP_YEAST
  tRNA CCA-pyrophosphrylase tRNA nucleotidyltransferase/poly(A) polymerase family 3ovb A 1.95 CCA_ARCFU
  ubiquitin-activating enzyme E1C (Uba3) ubiquitin-activating E1 family 1r4n B 3.60 UBA3_HUMAN
  ubiquitin-like 2 activating enzyme E1B ubiquitin-activating E1 family 1y8q D 2.25 ULE1B_HUMAN
  ubiquitin-like modifier-activating enzyme 5 ubiquitin-activating E1 family 3h8v A 2.00 UBA5_HUMAN
  biotin protien ligase not classified 2dto A 1.50 O57883_PYRHO
  FMN adenylyltransferase not classified 3g59 A 1.87 Q6FNA9_CANGA

ATP hydrolysis, PPPi is relased and adenosine is transferred (adenosylation)
  Protein Name Family PDB ID chain resol Uniprot ID

  methionine adenosyltransferase AdoMet synthse family 1o9t A 2.90 METK1_RAT
  CoB(I)alamin adenosyltransferase Cob(I)alamin adenosyltransferase family 1g5t A 1.80 BTUR_SALTY
  CoB(I)yrinic acid A,C-diamide adenosyltransferase Cob(I)alamin adenosyltransferase family 2idx A 2.50 MMAB_HUMAN

Others
  Protein Name Family PDB ID chain resol Uniprot ID

  7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK family 1dy3 A 2.00 HPPK_ECOLI
  Preneck appendage protein not classified 3gqn A 2.15 B3VMP8_BPPH2
  ATPsynthase epsilon subunit ATPase epsilon chain family 2e5y A 1.92 ATPE_BACP3
  Eukaryotic peptide chain release factor subunit 1 eukaryotic release factor 1 family 3e1y A 3.80 ERF1_HUMAN
  prabable ATP-dependent RNA helicase Ddx58 helicase family 3lrr A 2.15 DDX58_HUMAN
  NAD-dependent malic enzyme malic enzymes family 1gz4 A 2.20 MAOM_HUMAN
  DCP2 protein Nudix hydrolase family 2qkm B 2.80 DCP2_SCHPO
  acetylglutamate kinase-like protein P(II) protein family 2rd5 D 2.51 GLNB_ARATH
  STRADalpha STE Ser/Thr protein kinase family 3gni B 2.35 STRAA_HUMAN
  redox-sensing transcriptional repressor Rex transcriptional regulatory rex family 2vt3 B 2.00 REX_BACSU
  transient receptor potential cation channel subfamily V member 1 transient receptor 2pnn A 2.70 TRPV1_RAT
  polyhedrin not classified 2oh5 A 1.98 O10693_CPVBM
  pertussis toxin subunit 4 not classified 1bcp E 2.70 TOX4_BORPE
  non-biological protein not classified 2p09 A 1.65
  5′-AMP-activated protein kinase catalytic subunit alpha-1 5′-AMP-activated protein kinase gamma subunit family 2v92 E 2.40 AAKG1_RAT
  apoptosis regulator Ced4 AAA+ family/CARD domain/NB-ARC domain 2a5y B 2.60 CED4_CAEEL
  Clp1(inactive form) Clp1 family 2npi A 2.95 CLP1_YEAST
  Rck dmain of YuaA protein ktrA potassium transport (TC 2.A.38.4) family 2hmu A 2.25 KTRA_BACSU
  nitrogen regulatory protein P-II P(II) protein family 2xbp A 1.20 GLNB_SYNE7
  O-sialoglycoprotien endopeptidase (probably miss annotation, in reality, AP endonuclease) peptidase M22 family 2ivp A 2.50 GCP_PYRAB
  Rat synapsin I synapsin family 1pk8 A 2.10 SYN1_RAT
  putative uncharacterized protein TTHA0350 not classified 3ab8 A 1.70 Q5SLE3_THET8
  phosphofruktokinase not classified 3opy B 3.05 Q8TGA0_PICPA
  chloride channel protein 5 (clc-5) chloride channel family 2j9l C 2.30 CLCN5_HUMAN
  gluconate kinase FGGY kinase family 3ll3 A 2.00 Q5FM28_LACAC
  Hypothetical protein YfbG fmt family/ sugar epimerase familiy 1z7e D 3.00 ARNA_ECOLI
  ATP-dependent molecular chaperone Hsp82 heat shock protein 90 family 2cg9 B 3.10 HSP82_YEAST
  DNA packaging protein Gp17 myoviridae large terminase family 2o0h A 1.88 TERL_BPT4
  AP4a hydrolase Nudix hydrolase family 2pq1 A 1.95 O66548_AQUAE
  aspartate carbamoyltransferase regulatory chain (PyrI) PyrI family 2yww B 2.00 PYRI_METJA
  ribonucleotide reductase R1 ribonucleoside diphosphate reductase large chain family 3r1r A 3.00 RIR1_ECOLI
  SMC protein SMC family 1xex A 2.50 SMC_METJA
  molybdenum storage protein subunit alpha UMP kinase family 2ogx A 1.60 MOSA_AZOVD
  uncharacterized protein universal stress protein A family 3cis G 2.90 O06189_MYCTU
  Actin-depolymerizing factor Brevin villin/gelsolin family 2fgh A 2.80 GELS_HORSE
  ethanolamine utilization protein EutJ not classified 3h1q A 2.80
  universal stress protein F not classified 3fdx A 1.58 A6T8F5_KLEP7
  alcaligin biosynthesis protein not classified 2x0q A 1.96 P94255_BORBR
  l-proline dehydrogenase alpha subunit not classified 1y56 A 2.86 O59088_PYRHO
  FtsA not classified 1e4g T 2.60 Q9WZU0_THEMA
  NTRC-like two-domain protein not classified 3fkq A 2.10
  hemerythrin-like domain protein DcrH not classified 3a8t A 2.37 Q9REU3_DESVU
  Protein Mj1225 not classified 3lfz A 2.20 Y1225_METJA
  pyridoxal kinase not classified 3ibq A 2.00 Q88YB5_LACPL
  ATP:CoB(I)alamin adenosyltransferase not classified 2zhz A 1.80 Q2SZ09_BURTA
  clbalamin adenosyltransferase PduO-like protein not classified 3gah A 1.17 Q50EJ2_LACRE
  putative ribokinase II not classified 3iq0 B 1.79 Q8FD38_ECOL6
  Universal stress protein family not classified 2z08 A 1.55 Q5SJV7_THET8
  phosphofruktokinase not classified 3ie7 A 1.60 Q929S5_LISIN
  achromobactin synthetase protein D (ACSD) not classified 2x3j A 2.00 Q93AT8_ERWCH
  MccB not classified 3h5n A 1.90 Q47506_ECOLX
  HipA not classified 3dnt B 1.66 HIPA_ECOLI
  pyruvate carboxylase not classified 3bg5 A 2.80 Q99UY8_STAAM
  probable ATP-dependent DNA ligase D not classified 2faq A 1.90 Q9I1X7_PSEAE
  ParA ATPase not classified 3ea0 B 2.20 Q8KF94_CHLTE
  small nucleolar RNP similar to Gar1 not classified 2hvy B 2.30 Q8U029_PYRFU