SCOPe 2.02: Family c.56.5.4: Bacterial dinuclear zinc exopeptidases

Lineage for Family c.56.5.4: Bacterial dinuclear zinc exopeptidases

1. Root: SCOPe 2.02

2. Class c: Alpha and beta proteins (a/b) [51349] (147 folds)

3. Fold c.56: Phosphorylase/hydrolase-like [53162] (8 superfamilies)
   core: 3 layers, a/b/a ; mixed sheet of 5 strands: order 21354; strand 4 is antiparallel to the rest; contains crossover loops

4. Superfamily c.56.5: Zn-dependent exopeptidases [53187] (10 families)
   core: mixed beta-sheet of 8 strands, order 12435867; strands 2, 6 & 7 are antiparallel to the rest

5. Family c.56.5.4: Bacterial dinuclear zinc exopeptidases [53204] (18 proteins)

Proteins:

1. Allantoate amidohydrolase AllC catalytic domain [142514] (1 species)

   • Species Escherichia coli [TaxId:562] [142515] (2 PDB entries)
     Uniprot P77425 2-210,328-411

2. Aminoacylase-1, catalytic domain [102511] (1 species)

   • Species Human (Homo sapiens) [TaxId:9606] [102512] (1 PDB entry)

3. Aminopeptidase [53205] (2 species)

   1. Species Aeromonas proteolytica [TaxId:671] [53206] (17 PDB entries)
      Uniprot Q01693
      synonym: Vibrio proteolyticus

   2. Species Streptomyces griseus [TaxId:1911] [53207] (5 PDB entries)

4. Aminopeptidase PepV [82450] (1 species)
   unspecific amino dipeptidase

   • Species Lactobacillus delbrueckii [TaxId:1584] [82451] (1 PDB entry)

5. Aminopeptidase YpdE [142520] (1 species)

   • Species Shigella flexneri [TaxId:623] [142521] (1 PDB entry)
     Uniprot Q83K87 1-66,148-345
     hypothetical protein SF2450 (PDB)/SF2449.1 (UniProt)

6. Carboxypeptidase G2, catalytic domain [53208] (1 species)

   • Species Pseudomonas sp., strain rs-16 [TaxId:306] [53209] (1 PDB entry)

7. Deblocking aminopeptidase YhfE [142512] (1 species)
   contains insert beta-barrel domain

   • Species Bacillus cereus [TaxId:1396] [142513] (1 PDB entry)
     Uniprot Q81HB5 3-73,187-348
     BC0901

8. Endoglucanase TM1049 [142516] (1 species)

   • Species Thermotoga maritima [TaxId:2336] [142517] (1 PDB entry)
     Uniprot Q9X0D9 1-64,149-339

9. Frv operon protein FrvX, catalytic domain [117659] (1 species)

   • Species Pyrococcus horikoshii [TaxId:53953] [117660] (3 PDB entries)
     Uniprot O59196 # PH1527

10. Hypothetical protein YsdC, catalytic domain [102513] (1 species)
    contains insert beta-barrel domain

    • Species Bacillus subtilis [TaxId:1423] [102514] (1 PDB entry)

11. IAA-amino acid hydrolase, catalytic domain [117663] (1 species)

    • Species Mouse-ear cress (Arabidopsis thaliana) [TaxId:3702] [117664] (2 PDB entries)
      Uniprot P54970 37-428

12. Peptidase T (tripeptidase), catalytic domain [75250] (2 species)

    1. Species Escherichia coli [TaxId:562] [102506] (1 PDB entry)

    2. Species Salmonella typhimurium [TaxId:90371] [75251] (1 PDB entry)

13. Peptidase-like beta-alanine synthase, catalytic domain [102507] (1 species)

    • Species Yeast (Saccharomyces kluyveri) [TaxId:4934] [102508] (2 PDB entries)

14. Probable aminopeptidase ApeA [117661] (1 species)
    contains insert beta-barrel domain

    • Species Lyme disease spirochete (Borrelia burgdorferi) [TaxId:139] [117662] (1 PDB entry)
      Uniprot Q45055

15. Protein YxeP [142518] (1 species)

    • Species Bacillus subtilis [TaxId:1423] [142519] (1 PDB entry)
      Uniprot P54955 4-177,293-379

16. Putative endoglucanase TM1048, catalytic domain [102515] (1 species)
    contains insert beta-barrel domain

    • Species Thermotoga maritima [TaxId:2336] [102516] (1 PDB entry)

17. Succinyl-diaminopimelate desuccinylase, catalytic domain [102509] (1 species)

    • Species Neisseria meningitidis [TaxId:487] [102510] (1 PDB entry)

18. automated matches [190049] (2 species)
    not a true protein

    1. Species Streptomyces griseus [TaxId:1911] [186770] (6 PDB entries)

    2. Species Vibrio proteolyticus [TaxId:671] [186859] (5 PDB entries)

More info for Family c.56.5.4: Bacterial dinuclear zinc exopeptidases

Timeline for Family c.56.5.4: Bacterial dinuclear zinc exopeptidases:

• Family c.56.5.4: Bacterial dinuclear zinc exopeptidases first appeared (with stable ids) in SCOP 1.55, called Family c.56.5.4: Bacterial exopeptidases
  
• Family c.56.5.4: Bacterial dinuclear zinc exopeptidases appears in SCOPe 2.01
  
• Family c.56.5.4: Bacterial dinuclear zinc exopeptidases appears in SCOPe 2.03
  
• Family c.56.5.4: Bacterial dinuclear zinc exopeptidases appears in the current release, SCOPe 2.08