SCOPe 2.08: Family d.20.1.1: UBC-related

Lineage for Family d.20.1.1: UBC-related

1. Root: SCOPe 2.08

2. Class d: Alpha and beta proteins (a+b) [53931] (396 folds)

3. Fold d.20: UBC-like [54494] (1 superfamily)
   alpha-beta(4)-alpha(3); core: meander beta-sheet plus one helix 2

4. Superfamily d.20.1: UBC-like [54495] (5 families)

5. Family d.20.1.1: UBC-related [54496] (7 proteins)

Proteins:

1. Hypothetical protein Tgtwinscan_2721, E2 domain [143066] (1 species)

   • Species Toxoplasma gondii [TaxId:5811] [143067] (1 PDB entry)

2. Putative ubiquitin-conjugating enzyme, E2 domain [143070] (1 species)

   • Species Plasmodium chabaudi [TaxId:5825] [143071] (1 PDB entry)
     Uniprot Q4Y037 88-196

3. Ubiquitin conjugating enzyme, UBC [54497] (34 species)

   1. Species African clawed frog (Xenopus laevis) [TaxId:8355] [160080] (1 PDB entry)

   2. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [187672] (2 PDB entries)

   3. Species Baker's yeast (Saccharomyces cerevisiae), mms2 [TaxId:4932] [64241] (2 PDB entries)

   4. Species Baker's yeast (Saccharomyces cerevisiae), ubc1 [TaxId:4932] [69685] (3 PDB entries)
      Uniprot P21734

   5. Species Baker's yeast (Saccharomyces cerevisiae), ubc13 [TaxId:4932] [64239] (5 PDB entries)

   6. Species Baker's yeast (Saccharomyces cerevisiae), ubc2 (RAD6) [TaxId:4932] [54499] (1 PDB entry)

   7. Species Baker's yeast (Saccharomyces cerevisiae), ubc4 [TaxId:4932] [54500] (1 PDB entry)

   8. Species Baker's yeast (Saccharomyces cerevisiae), ubc7 [TaxId:4932] [54501] (1 PDB entry)

   9. Species Caenorhabditis elegans, E2 2 [TaxId:6239] [143060] (1 PDB entry)
      Uniprot P35129 1-147

   10. Species Clam (Spisula solidissima), E-2C [TaxId:6584] [54504] (2 PDB entries)

   11. Species Human (Homo sapiens) [TaxId:9606] [385992] (1 PDB entry)

   12. Species Human (Homo sapiens), E2 D3 [TaxId:9606] [143054] (3 PDB entries)
       Uniprot P61077 1-147

   13. Species Human (Homo sapiens), E2 G1 [TaxId:9606] [143056] (1 PDB entry)
       Uniprot P62253 7-131

   14. Species Human (Homo sapiens), E2 H [TaxId:9606] [143055] (2 PDB entries)
       Uniprot P62256 4-155

   15. Species Human (Homo sapiens), E2 J2 [TaxId:9606] [143050] (1 PDB entry)
       Uniprot Q5T7L1 12-168
       ubc6 homologue

   16. Species Human (Homo sapiens), E2 L6 [TaxId:9606] [143052] (1 PDB entry)
       Uniprot O14933 2-151

   17. Species Human (Homo sapiens), E2 M [TaxId:9606] [143058] (3 PDB entries)
       Uniprot P61081 27-183
       the extra N-terminal peptide, bound to the heterodimeric E1 enzyme for NEDD8, can be seen in the PDB entry 1tt5, chains E and F

   18. Species Human (Homo sapiens), E2 S [TaxId:9606] [143048] (1 PDB entry)
       Uniprot Q16763 6-156

   19. Species Human (Homo sapiens), E2 T [TaxId:9606] [143057] (1 PDB entry)
       Uniprot Q9NPD8 1-154
       Hspc150

   20. Species Human (Homo sapiens), E2 U [TaxId:9606] [143053] (1 PDB entry)
       Uniprot Q5VVX9 1-148

   21. Species Human (Homo sapiens), E2 variant 1 [TaxId:9606] [143051] (7 PDB entries)
       Uniprot Q13404 80-221! Uniprot Q13404 82-220

   22. Species Human (Homo sapiens), mms2 [TaxId:9606] [64242] (6 PDB entries)

   23. Species Human (Homo sapiens), ubc13 [TaxId:9606] [64240] (23 PDB entries)

   24. Species Human (Homo sapiens), ubc2b [TaxId:9606] [102840] (4 PDB entries)
       E2-17 kDa

   25. Species Human (Homo sapiens), ubc9 [TaxId:9606] [54503] (29 PDB entries)
       identical sequence in many other species

   26. Species Human (Homo sapiens), ubch10 [TaxId:9606] [64243] (1 PDB entry)

   27. Species Human (Homo sapiens), ubch5b [TaxId:9606] [102841] (31 PDB entries)
       Uniprot P62837
       E2-17 kDa 2

   28. Species Human (Homo sapiens), ubch7 [TaxId:9606] [54502] (2 PDB entries)

   29. Species Human (Homo sapiens), ubch8 [TaxId:9606] [117850] (1 PDB entry)
       Uniprot Q96LR5 54-201

   30. Species Leishmania major [TaxId:5664] [143049] (1 PDB entry)
       Uniprot Q4Q5L3 9-166
       Ubiquitin carrier protein 4, putative

   31. Species Nematode (Caenorhabditis elegans), E2-19 kDa [TaxId:6239] [89862] (1 PDB entry)

   32. Species Nematode (Caenorhabditis elegans), E2-21.5 kDa [TaxId:6239] [102842] (1 PDB entry)

   33. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [54498] (1 PDB entry)

   34. Species Toxoplasma gondii [TaxId:5811] [143059] (1 PDB entry)

4. Ubiquitin-conjugating enzyme E2 Q2, C-terminal domain [143068] (1 species)
   this proteins contains the N-terminal RWD domain

   • Species Human (Homo sapiens) [TaxId:9606] [143069] (1 PDB entry)
     Uniprot Q8WVN8 201-362

5. Ubiquitin-conjugating enzyme E2-25 kDa, E2 domain [143063] (2 species)
   ubc1 homologue; also contains the C-terminal UBA domain

   1. Species Cow (Bos taurus) [TaxId:9913] [143065] (1 PDB entry)
      Uniprot P61085 1-154

   2. Species Human (Homo sapiens) [TaxId:9606] [143064] (10 PDB entries)
      Uniprot P61086 1-156

6. Ubiquitin-protein ligase W (E2 W) [143061] (1 species)
   forms segment-swapped dimer

   • Species Human (Homo sapiens) [TaxId:9606] [143062] (1 PDB entry)
     Uniprot Q96B02 1-117

7. automated matches [190124] (13 species)
   not a true protein

   1. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:4932] [189599] (2 PDB entries)

   2. Species Baker's yeast (Saccharomyces cerevisiae) [TaxId:559292] [197196] (4 PDB entries)

   3. Species Entamoeba (Entamoeba histolytica) [TaxId:5759] [193761] (1 PDB entry)

   4. Species Fission yeast (Schizosaccharomyces pombe) [TaxId:4896] [189937] (1 PDB entry)

   5. Species Human (Homo sapiens) [TaxId:9606] [186848] (52 PDB entries)

   6. Species Leishmania major [TaxId:5664] [188133] (1 PDB entry)

   7. Species Mouse (Mus musculus) [TaxId:10090] [188773] (1 PDB entry)

   8. Species Nematode (Brugia malayi) [TaxId:6279] [226704] (1 PDB entry)

   9. Species Nematode (Caenorhabditis elegans) [TaxId:6239] [186897] (1 PDB entry)

   10. Species Plasmodium falciparum [TaxId:36329] [187963] (5 PDB entries)

   11. Species Schizosaccharomyces pombe [TaxId:284812] [196618] (2 PDB entries)

   12. Species Thale cress (Arabidopsis thaliana) [TaxId:3702] [370009] (2 PDB entries)

   13. Species Zebrafish (Danio rerio) [TaxId:7955] [188346] (1 PDB entry)

More info for Family d.20.1.1: UBC-related

Timeline for Family d.20.1.1: UBC-related:

• Family d.20.1.1: UBC-related first appeared (with stable ids) in SCOP 1.55, called Family d.20.1.1: Ubiquitin conjugating enzyme
  
• Family d.20.1.1: UBC-related appears in SCOPe 2.07