SCOPe 2.04: Family d.3.1.1: Papain-like

Lineage for Family d.3.1.1: Papain-like

1. Root: SCOPe 2.04

2. Class d: Alpha and beta proteins (a+b) [53931] (380 folds)

3. Fold d.3: Cysteine proteinases [54000] (1 superfamily)
   consists of one alpha-helix and 4 strands of antiparallel beta-sheet and contains the catalytic triad Cys-His-Asn

4. Superfamily d.3.1: Cysteine proteinases [54001] (23 families)
   the constitute families differ by insertion into and circular permutation of the common catalytic core made of one alpha-helix and 3-strands of beta-sheet

5. Family d.3.1.1: Papain-like [54002] (26 proteins)

Proteins:

1. (Pro)cathepsin B [54022] (3 species)

   1. Species Cow (Bos taurus) [TaxId:9913] [54025] (3 PDB entries)

   2. Species Human (Homo sapiens) [TaxId:9606] [54023] (6 PDB entries)

   3. Species Norway rat (Rattus norvegicus) [TaxId:10116] [54024] (4 PDB entries)

2. (Pro)cathepsin K [54028] (2 species)

   1. Species Human (Homo sapiens) [TaxId:9606] [54029] (42 PDB entries)
      Uniprot P43235 116-329 ! Uniprot P43235 115-329

   2. Species Rabbit (Oryctolagus cuniculus) [TaxId:9986] [142845] (1 PDB entry)
      Uniprot P43236 115-329

3. (Pro)cathepsin L [54026] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [54027] (4 PDB entries)

4. (Pro)cathepsin S [82566] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [82567] (23 PDB entries)

5. (Pro)cathepsin V [64202] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [64203] (3 PDB entries)

6. (Pro)cathepsin X [54031] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [54032] (2 PDB entries)

7. Actinidin [54003] (1 species)

   • Species Chinese gooseberry or kiwifruit (Actinidia chinensis) [TaxId:3625] [54004] (2 PDB entries)

8. Bleomycin hydrolase [54017] (2 species)
   DNA-binding protease that has more insertions in the papain-like fold

   1. Species Baker's yeast (Saccharomyces cerevisiae), Gal6 [TaxId:4932] [54018] (9 PDB entries)

   2. Species Human (Homo sapiens) [TaxId:9606] [54019] (2 PDB entries)

9. Caricain (protease omega) [54007] (1 species)

   • Species Papaya (Carica papaya) [TaxId:3649] [54008] (3 PDB entries)

10. Cathepsin C (dipeptidyl peptidase I), catalytic domain [75330] (2 species)

    1. Species Human (Homo sapiens) [TaxId:9606] [75331] (1 PDB entry)

    2. Species Norway rat (Rattus norvegicus) [TaxId:10116] [82565] (1 PDB entry)

11. Cathepsin F [89805] (1 species)

    • Species Human (Homo sapiens) [TaxId:9606] [89806] (1 PDB entry)

12. Cathepsin H [81637] (1 species)
    also contains a disulfide-bound minicathepsin H chain

    • Species Pig (Sus scrofa) [TaxId:9823] [81636] (3 PDB entries)

13. Chymopapain [54009] (1 species)

    • Species Papaya (Carica papaya) [TaxId:3649] [54010] (1 PDB entry)

14. Cruzain [54020] (1 species)

    • Species Trypanosoma cruzi [TaxId:5693] [54021] (20 PDB entries)

15. Ervatamin B [89803] (1 species)

    • Species Adam's apple (Ervatamia coronaria) [TaxId:52861] [89804] (1 PDB entry)

16. Ervatamin C [102717] (1 species)

    • Species East indian rosebay (Ervatamia coronaria) [TaxId:52861] [102718] (1 PDB entry)

17. Falcipain 2 [142846] (1 species)

    • Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [142847] (5 PDB entries)
      Uniprot Q9N6S8 244-484

18. Glycyl endopeptidase [54011] (1 species)

    • Species Papaya (Carica papaya) [TaxId:3649] [54012] (1 PDB entry)

19. Major mite fecal allergen der p 1 [142848] (1 species)

    • Species House-dust mite (Dermatophagoides pteronyssinus) [TaxId:6956] [142849] (3 PDB entries)
      Uniprot P08176 19-320! Uniprot P08176 99-320

20. Papain [54005] (1 species)

    • Species Papaya (Carica papaya) [TaxId:3649] [54006] (23 PDB entries)

21. Proline-specific cysteine protease [54013] (1 species)

    • Species Ginger rhizome (Zingiber officinale) [TaxId:94328] [54014] (1 PDB entry)

22. Staphopain SspB [102721] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [102722] (3 PDB entries)
      Uniprot Q70UQ9 41-393

23. Staphopain StpA [54033] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [54034] (1 PDB entry)

24. Streptococcal pyrogenic exotoxin B [54035] (1 species)

    • Species Streptococcus pyogenes [TaxId:1314] [54036] (2 PDB entries)
      Uniprot P00788 31-398

25. Vignain (bean endopeptidase) [102719] (1 species)

    • Species Castor bean (Ricinus communis) [TaxId:3988] [102720] (1 PDB entry)

26. automated matches [190264] (9 species)
    not a true protein

    1. Species Actinidia arguta [TaxId:64478] [189532] (4 PDB entries)

    2. Species Carica candamarcensis [TaxId:35926] [189214] (1 PDB entry)

    3. Species Cow (Bos taurus) [TaxId:9913] [187053] (8 PDB entries)

    4. Species Human (Homo sapiens) [TaxId:9606] [187102] (7 PDB entries)

    5. Species Jacaratia mexicana [TaxId:309130] [187452] (1 PDB entry)

    6. Species Malaria parasite (Plasmodium falciparum) [TaxId:5833] [188686] (2 PDB entries)

    7. Species Mouse (Mus musculus) [TaxId:10090] [229208] (5 PDB entries)

    8. Species Tabernaemontana divaricata [TaxId:52861] [187993] (3 PDB entries)

    9. Species Trypanosoma brucei [TaxId:31286] [188393] (2 PDB entries)

More info for Family d.3.1.1: Papain-like

Timeline for Family d.3.1.1: Papain-like:

• Family d.3.1.1: Papain-like first appeared (with stable ids) in SCOP 1.55
  
• Family d.3.1.1: Papain-like appears in SCOPe 2.03
  
• Family d.3.1.1: Papain-like appears in SCOPe 2.05
  
• Family d.3.1.1: Papain-like appears in the current release, SCOPe 2.08