Table 2.
Natural classification of the β-GF.
| I. Basal 4-stranded versions of the β-GF |
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| A. Archaeo-eukaryotic RNA polymerase β-subunit domain superfamily (all eukaryotes, all archaea) function unknown |
| PDB: 1I6HB (residues ~573–631) |
| B. IF3-N terminal domain superfamily (all bacteria, all eukaryotes except Giardia) function unknown |
| PDB: 1TIF (residues ~9–61) |
| C. POZ superfamily (all eukaryotes) mediates dimerization and transcriptional repression and interacts with histone deacetylase co-repressor complexes |
| PDB: 1HV2, several others |
| D. BofC/IGB lineage |
| Bypass of forespore (Bof)C family (Bacillus, Geobacillus) secreted protein important in spore formation pathway |
| PDB: 2BW2 |
| Immunoglobulin-binding (Ig-binding) family (firmicutes) cell surface virulence protein |
| PDB: 1HEZ, several others |
| E. Other lineages |
| Yml108w family (budding yeast) function unknown |
| PDB: 1N6Z |
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|
| II. Nudix (MutT) Superfamily |
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| (all eukaryotes, crenarchaea, euryarchaea, all bacteria, dsDNA viruses) nucleotide-derivative phosphohydrolase, contains insert in middle of second strand |
| PDB: 1RYAA, several others |
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|
| III. Fasciclin-like assemblage |
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| A. Glutamine synthetase N-terminal domain (GS-N) superfamily (all eukaryotes except Giardia, crenarchaea, euryarchaea, all bacteria, mimivirus) two-stranded insert contributes residue to enzyme active site, forms one wall in active site |
| PDB: 2BVCA (residues ~17–100), several others |
| B. Phosphoribosyl AMP cyclohydrolase (HisI) superfamily (fungi, plants, crenarchaea, euryarchaea, all bacteria) Two enzyme active sites formed by an obligate HisI dimer |
| PDB: 1ZPS |
| C. Fasciclin I superfamily (apicomplexa, crown group, euryarchaea, actinobacteria, bacteroidetes, chlorobi, chlamydiae, chloroflexi, cyanobacteria, deinococci, acidobacteria, planctomycetes, α/β/δ/γ proteobacteria) binds sugar moieties |
| PDB: 1NYO, 1O70 |
| D. Ribosomal protein L25 superfamily (apicomplexa, plants, slime molds, Anopheles, all bacteria) binds 5S rRNA |
| PDB: 1DFU, several others |
| E. FimD N-terminal domain (FimD-N) superfamily (α/β/δ/γ proteobacteria, deinococci) interacts with FimC protein |
| PDB: 1ZE3, 1ZDV, 1ZDX |
| F. WWE superfamily (all eukaryotes except Giardia) |
| PDB: 2A90A |
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| IV. 5-stranded assemblage: Classical 5-stranded clade |
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| A. TGS superfamily (all eukaryotes, all archaea, all bacteria) |
| PDB: 1NYR (residues 1–62), several others |
| B. ThiS superfamily (crenarchaea, euryarchaea, all bacteria, algae, Thalassiosira, Emiliania, Phaeodactylum, Odontella). SAMP2 is conjugated |
| PDB: 1F0Z, many others |
| C. MoaD superfamily (crenarchaea, euryarchaea, all bacteria, crown group) SAMP1 is conjugated |
| PDB: 1FM0, many others |
| D. Urm-1 superfamily (all eukaryotes) conjugated version implicated in tRNA thiouridine synthesis, conjugated during oxidative stress response |
| PDB: 1XO3, 1WGK, 2AX5 |
| E. Mut7-C family (Bacteria) Often Fused to N-terminal PIN nuclease domain and C-terminal Zn-ribbon |
| F. Ribosomal protein S4 superfamily (all eukaryotes, all archaea, all bacteria) |
| PDB: 2CQJA |
| G. Aldehyde oxidoreductase N-terminal (AOR-N) domain superfamily (crenarchaea, euryarchaea, actinobacteria, chloroflexi, deinococci, firmicutes, α/β/δ/ε/γ proteobacteria) tandem repeats in same protein form dimer that recognizes metallopterins |
| PDB: 1AOR (residues 1–210) |
| H. Prokaryotic UB-like superfamily (See text for details) |
| YukD family (actinobacteria, firmicutes) |
| PDB: 2BPS |
| I. UB-like superfamily (see section VI. below) |
| J. SPK/SupAnt lineage |
| Strepto/staphylococcus kinase (SPK) family (Streptococcus, Staphylococcus, caudovirales) interacts with host plasmin protein, promoting virulence |
| PDB: 2SAK, several others |
| Superantigen (SupAnt) family (Staphylococcus, Streptococcus) interacts with T-cell receptor β-chains |
| PDB: 1TY0 (residues 104–211), several others |
| K. Other lineages of note |
| TmoB family (actinobacteria, α/β/γ proteobacteria) |
| PDB: 1T0Q, 1T0R, 1T0S |
| PHH-γ family (actinobacteria, β/γ proteobacteria) |
| PDB: 2inp-E |
| RnfH family (α/β/γ proteobacteria) |
| FliD-FlgL/K family (α/β/δ/ε proteobacteria, clostridia, planctomycetes, Thermotoga, spirochetes, acidobacteria, Mu-like phages) |
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| V. 5-stranded assemblage: Soluble ligand binding or metal chelating clade |
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| A. 2Fe-2S ferredoxin superfamily |
| 2Fe-2S family (all eukaryotes, all archaea, all bacteria) small insert with conserved cysteines chelates Fe ions |
| PDB: 1NEK (residues 1–106), several others |
| L-proline dehydrogenase-type oxidoreductase (L-proDH alpha) family (euryarchaea, Thermofilum, actinobacteria, firmicutes, Psychroflexus, Herpetosiphon, α/β/δ/γ proteobacteria) lack conserved cysteine residues |
| PDB: 1Y56A (residues ~10–94) |
| B. Molybdopterin-dependent oxidoreductase (SOX) superfamily (Toxoplasma, crown group, crenarchaea, euryarchaea, actinobacteria, Aquifex, bacteroidetes/chlorobi, chloroflexi, cyanobacteria, deinoccoci, acidobacteria, firmicutes, planctomycetes, α/β/δ/ε proteobacteria) two inserts in core β-sheet help facilitate enzymatic activity |
| PDB: 1SOX (residues ~150–310) |
| C. Soluble-ligand binding β-grasp (SLBB) superfamily |
| Nqo1 family (kinetoplastids, ciliates, crown group, euryarchaea, all bacteria) |
| PDB: 2FUGS (residues ~246–334) |
| Transcobalamin family (hexapoda, vertebrates, euryarchaea, firmicutes, planctomycetes) |
| PDB: 2BBC (residues ~330–415) |
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|
| VI. UB-like superfamily members |
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| A. Classic UB-like clade |
| NIP45/Reni family (crown group) |
| SUMO/SMT3 family (all eukaryotes) conjugated versions tag proteins for localization/regulation |
| PDB: 1TGZ, several others |
| ZFAND1-C family (Naegleria, apicomplexa, stramenopiles, crown group) fused to N-terminal AN1 treble-clef domains |
| UFD of E1 C-terminal UB-like domain family (all eukaryotes) C-terminal adaptor domain of E1-like enzymes that bind E2-like enzymes |
| PDB: 1Y8X |
| UBX family (all eukaryotes except Giardia) adaptor version receptor for protein processing and degradation via the ERAD system |
| PDB: 1H8C, several others |
| Rad23N family (all eukaryotes except Giardia) involved in protein recruitment to the proteosome |
| PDB : 1UEL, 1P1A |
| Sin3a/SAP18-Ddi1 family |
| Sin3a/SAP18 subfamily (Trichomonas, apicomplexa, ciliates, crown group) |
| PDB: 2HDE |
| DNA damage inducible 1 (Ddi1) subfamily (plants, fungi, animals) adaptor version regulating Ho interaction with proteosome |
| PDB: 1V5O |
| Apg8-Apg12-APG5 family |
| Apg8 subfamily (Trichomonas, Naegleria, kinetoplastids, apicomplexa, ciliates, Phytophthora, crown group, pestiviruses, Marseillevirus) target lipids to autophagy pathway |
| Apg12 subfamily (Trichomonas, Naegleria, ciliates, crown group) targets proteins to autophagy pathway |
| PDB: 1WZ3 |
| APG5 subfamily (Trichomonas kinetoplastids, apicomplexa, ciliates, entamoebidae, crown group) |
| PDB: 2DYM |
| Bmi1/Psc-Wdr48C family |
| Bmi1/Psc subfamily (apicomplexa, ciliates, plants, animals) |
| Wdr48 C-terminal UB-domain subfamily (crown group) |
| BIPOSTO/ARF-PB1 family |
| BIPOSTO/ARF subfamily (plants) plant transcription factor |
| PB1 subfamily (all eukaryotes except Giardia and Trichomonas) adaptor that regulates localization |
| PDB: 2BKF, several others |
| MUBs family (plants, fungi, animals) versions anchored to plasma membrane via prenylation |
| PDB: 1WHG, 1SEH9 |
| Nedd8 family (crown group) |
| PDB: 1NDD, others |
| BAG N-terminal domain family (plants, animals) adaptor version mediating proteosome and Hsc70/Hsp70 chaperone system interaction |
| PDB: 1WXV |
| ANKRD40 C-terminal domain family (animals,plants, slime molds) adaptor version fused to N-terminal ankyrin repeats or MJ1566-like domains |
| CP2 C-terminal domain family (fungi, animals) adaptor version fused to N-terminal P53-like DNA binding domains of the cytochrome F fold |
| Splicing factor 3a (Sf3a)/prp21 family (plants, animals) |
| PDB: 1WE7, 1ZKH |
| UBP11/Usp40N-GGNB1 family |
| Usp40 N-terminal UB domain subfamily (ciliates, slime molds, animals) |
| UBP11-GGNB1 UB domain subfamily (plants, slime molds, vertebrates) |
| Hepatocyte odd protein shuttling (HOPSP) family (animals) |
| PDB: 1WIA |
| Parkin family (entamoebidae, animals) adaptor that binds Rpn10 subunit of 26S proteosomal subunit |
| PDB: 1IYF, 1MG8 |
| S30 N-terminal fusion ribosomal protein (S30-N) family (animals) adaptor that associates with Bcl-G and histone 2A |
| Midnolin family (animals) regulates genes related to neurogenesis in the nucleolus |
| Bone marrow stromal cell-derived (BMSC) UB family (animals) may regulate BMSC function in cell differentiation |
| PDB: 1X1M |
| Dendritic cell-derived C-terminal (DC-C) UB domain family (animals) implicated in cell differentiation and apoptosis |
| TRS4 N-terminal domain UB family (animals) |
| PDB: 2DAF |
| IkappaB kinase beta (IKK) UB-like domain family (animals) domain required for kinase activity |
| GDX N-terminal domain family (fungi, animals) |
| Homocysteine-inducible, endoplasmic reticulum stress-inducible protein (Herp-1) UB domain family (animals) |
| AN1 UB-like domain family (animals) |
| Interferon-inducible protein (ISG-15) UB domain family (vertebrates) conjugated version that tags proteins as part of antiviral response pathway |
| PDB: 1Z2M |
| 2'–5' oligoadenylate synthetase-like protein C-terminal (Oasl2-C) UB domain family (vertebrates) interacts with MBD1 transcriptional repressor |
| PDB: 1WH3 |
| Classic UB family (all eukaryotes, Candidatus 'Caldiarchaeum subterraneum’ and certain viruses) conjugated versions modulating protein stability and interactions |
| PDB: 1XD3, many others |
| Sacsin UB-domain family (vertebrates) |
| Rb1cc1 family (animals) |
| FAT10/Diubiquitin family (slime molds, vertebrates) conjugated version that tags proteins for proteosomal degradation |
| Np95-like ring finger protein N-terminal (NIRF-N) UB domain family (vertebrates) |
| PDB: 1WY8, 2FAZ |
| HOIL-1 UB-like domain family (animals) adaptor protein that regulates degradation of suppressor of cytokine signaling (SOCS) proteins |
| Transcription elongation factor B (Elongin B) family (animals) positive regulator of RNA pol II elongation factor A, possible tumor and cytokine signaling complex suppressor, and hypoxia-inducible gene regulator |
| PDB: 1VCB, several others |
| Nedd8 ultimate buster-1 (NUB1L) N-terminal UB domain family (animals) adaptor version linking FAT10 with the 26S proteosome |
| PDB: 1WJU |
| Ubiquilin N-terminal UB domain family (animals) adaptor version that interacts with PDI and mediates delivery of tagged proteins to the proteosome |
| USP48/USP26 C terminal UB domain family (plants, animals) |
| U11/U12 snRNP 25K family (plants, animals) |
| PDB: 1V2Y |
| Glycoprotein, synaptic 2 N-terminal (Gpsn2-N) domain family (apicomplexa, plants, slime molds, animals) |
| Ubl5-HubA family |
| Ubl5 subfamily (Trichomonas, apicomplexa, crown group) possibly a conjugating version, although target unknown |
| HubA subfamily (Tetrahymena, fungi) appears to modify Snu66 in pre-mRNA splicing and localization, conjugates with cell polarity factors Sph1 and Hbt1 |
| TUG-UBL1 N-terminal UB domain family (Naegleria, slime molds, fungi, animals) |
| PDB: 2AL3 |
| CLU1/eIF-3 family (Naegleria, ciliates, crown group) |
| VCPIP1- HIP7PN family |
| Valosin-containing protein (p97)/p47 complex-interacting protein p135 (VCPIP1) UB domain subfamily (vertebrates) |
| HIV-induced protein-7-like protease N-terminal (HIP7P-N) UB-like domain subfamily (all eukaryotes except Giardia) |
| UBP7/UBP14N-Ublcp1-Atg35690N family |
| UBP7/UBP14 N-terminal UB domain subfamily (all eukaryotes except Giardia) likely adaptor protein binding to p53 |
| PDB: 1V86, 1WGG |
| Ublcp1 UB domain subfamily (crown group) |
| Atg35690 N-terminal UB domain subfamily (fungi, plants) |
| Bat3/DsK family (all eukaryotes) adaptor version that binds with Hsp70-like Stch |
| PDB: 1WX9, 2BWF, 2BWE |
| AT23465p C-terminal domain family (Trichomonas, Giardia, kinetoplastids, ciliates, animals) fused to cytochrome b5-like heme/steroid binding domain |
| TbcB-TbcE family |
| Tubulin binding cofactor B (TbcB) UB-like domain subfamily (all eukaryotes except Trichomonas) |
| PDB: 1T0Y, 1V6E |
| Tubulin binding cofactor E (TbcE) UB-like domain subfamily (kinetoplastids, ciliates, plants, animals) |
| PDB: 1WJN |
| B. RA/FERM/PI3KN/DWNN clade |
| Ras-associating (RA) family (slime molds, fungi, animals) |
| PDB: 1RAX, several others |
| FERM UB-like domain family(ciliates, plants, slime molds, entamoebidae, animals) |
| PDB: 1EF1 (residues 4–87), several others |
| Phosphoinositide 3-kinase N-terminal (PI3K-N) domain family (all eukaryotes) |
| PDB: 1E8Y (residues ~217–310), several others |
| DWNN (RBBP6 N-terminal domain) family (all eukaryotes except Giardia and kinetoplastids) |
| PDB: 27CH |
| C. CAD/DCX clade |
| CAD domain family (animals) adaptor version that inhibits DNAse activity |
| PDB: 1IBX, several others |
| Double cortin (DCX) domain family (all eukaryotes except Giardia) occur in tandem, function as microtubule-binding domains |
| D. Additional 5-stranded classical UB-like lineages |
| BM-002/Ufm1 family (all eukaryotes except Trichomonas) conjugated version |
| PDB: 1J0G |
| NPL4 N-terminal (NPL4-N) UB-like domain family (all eukaryotes) |
| PDB: 1WF9 |