SCOPe 2.01: Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase

Lineage for Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase

1. Root: SCOPe 2.01

2. Class e: Multi-domain proteins (alpha and beta) [56572] (66 folds)

3. Fold e.3: beta-lactamase/transpeptidase-like [56600] (1 superfamily)
   contains a cluster of helices and an alpha+beta sandwich

4. Superfamily e.3.1: beta-lactamase/transpeptidase-like [56601] (4 families)

5. Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase [56602] (19 proteins)

Proteins:

1. 6-aminohexanoate-dimer hydrolase NylC [160972] (1 species)
   NylB'

   • Species Flavobacterium sp. [TaxId:239] [160973] (11 PDB entries)
     Uniprot P07062 5-392

2. AMPC beta-Lactamase, class C [56618] (3 species)
   contains small alpha+beta subdomain inserted in the common fold

   1. Species Citrobacter freundii [TaxId:546] [56619] (3 PDB entries)

   2. Species Enterobacter cloacae, P99, cephalosporinase [TaxId:550] [56620] (8 PDB entries)
      Uniprot P05364 22-380 ! Uniprot P05364 22-381

   3. Species Escherichia coli, cephalosporinase [TaxId:562] [56621] (66 PDB entries)

3. beta-Lactamase, class A [56606] (15 species)

   1. Species Bacillus licheniformis [TaxId:1402] [56612] (9 PDB entries)

   2. Species Enterobacter cloacae, NMC-A carbapenemase [TaxId:550] [56613] (2 PDB entries)

   3. Species Escherichia coli, TEM-1 [TaxId:562] [56607] (33 PDB entries)

   4. Species Escherichia coli, TOHO-1 [TaxId:562] [56608] (15 PDB entries)

   5. Species Klebsiella pneumoniae, SHV-1 [TaxId:573] [56609] (14 PDB entries)
      inhibited by tazobactam
      Uniprot Q5PSW7 ! Uniprot P14557 22-286

   6. Species Klebsiella pneumoniae, SHV-2 [TaxId:573] [90082] (10 PDB entries)
      almost identical sequence to SHV-1

   7. Species Klebsiella pneumoniae, TEM52 [TaxId:573] [64473] (1 PDB entry)

   8. Species Mycobacterium fortuitum [TaxId:1766] [56615] (1 PDB entry)

   9. Species Proteus vulgaris [TaxId:585] [75596] (1 PDB entry)

   10. Species Pseudomonas aeruginosa, PER-1 [TaxId:287] [56616] (1 PDB entry)

   11. Species Pseudomonas aeruginosa, PSE-4 carbenicillinase [TaxId:287] [56610] (2 PDB entries)

   12. Species Serratia marcescens, Sme-1 [TaxId:615] [56617] (1 PDB entry)
       imipenem-hydrolyzing

   13. Species Staphylococcus aureus [TaxId:1280] [56611] (16 PDB entries)

   14. Species Stenotrophomonas maltophilia, L2 [TaxId:40324] [103374] (2 PDB entries)

   15. Species Streptomyces albus G [TaxId:1962] [56614] (1 PDB entry)

4. Class D beta-lactamase [56622] (4 species)

   1. Species Escherichia coli, OXA-1 [TaxId:562] [82837] (2 PDB entries)

   2. Species Pseudomonas aeruginosa, OXA-10 [TaxId:287] [56623] (25 PDB entries)

   3. Species Pseudomonas aeruginosa, OXA-13 [TaxId:287] [64474] (3 PDB entries)

   4. Species Salmonella typhimurium, OXA-2 [TaxId:90371] [90083] (1 PDB entry)

5. D,D-carboxypeptidase DacA, N-terminal domain [118181] (1 species)

   • Species Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [118182] (1 PDB entry)
     Uniprot P72518 25-393

6. D-ala carboxypeptidase/transpeptidase [56603] (2 species)

   1. Species Streptomyces sp., K15 [TaxId:1931] [56604] (7 PDB entries)

   2. Species Streptomyces sp., R61 [TaxId:1931] [56605] (14 PDB entries)
      Uniprot P15555 34-378 ! Uniprot P15555

7. D-Amino acid amidase DaaA [144038] (1 species)

   • Species Ochrobactrum anthropi [TaxId:529] [144039] (4 PDB entries)
     Uniprot Q9LCC8 2-363

8. D-aminopeptidase, N-terminal domain [56626] (1 species)

   • Species Ochrobactrum anthropi [TaxId:529] [56627] (1 PDB entry)

9. Esterase EstB [69873] (1 species)

   • Species Burkholderia gladioli [TaxId:28095] [69874] (2 PDB entries)

10. Pencillin binding protein 4 (PbpD), N-terminal domain [111287] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [111288] (1 PDB entry)
      Uniprot Q53613 21-383

11. Penicillin binding protein 2a (PBP2A), C-terminal domain [82838] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [82839] (5 PDB entries)
      Uniprot O54286 27-668

12. Penicillin receptor BlaR, C-terminal domain [103375] (1 species)
    closely related to class D beta-lactamase

    • Species Bacillus licheniformis [TaxId:1402] [103376] (1 PDB entry)

13. Penicillin-binding protein 1a, transpeptidase domain [144034] (1 species)

    • Species Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [144035] (2 PDB entries)
      Uniprot Q8DR59 266-650! Uniprot Q8DR59 267-650

14. Penicillin-binding protein 1b, transpeptidase domain [144036] (1 species)

    • Species Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [144037] (3 PDB entries)
      Uniprot O70038 337-789! Uniprot O70038 337-791

15. Penicillin-binding protein 2, PBP2 [160970] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [160971] (3 PDB entries)
      Uniprot Q2YY56 293-692

16. Penicillin-binding protein 2x (pbp-2x), transpeptidase domain [56624] (1 species)

    • Species Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [56625] (10 PDB entries)

17. Penicillin-binding protein 5, N-terminal domain [69875] (1 species)

    • Species Escherichia coli [TaxId:562] [69876] (8 PDB entries)

18. Regulatory protein BlaR1 [111289] (1 species)

    • Species Staphylococcus aureus [TaxId:1280] [111290] (3 PDB entries)
      Uniprot P18357 338-582 ! Uniprot P18357 334-581 ! Uniprot P18357 338-583

19. automated matches [190161] (13 species)
    not a true protein

    1. Species Bacillus licheniformis [TaxId:1402] [188244] (4 PDB entries)

    2. Species Citrobacter sedlakii [TaxId:67826] [188289] (3 PDB entries)

    3. Species Enterobacter cloacae [TaxId:550] [187307] (3 PDB entries)

    4. Species Escherichia coli [TaxId:469008] [188520] (1 PDB entry)

    5. Species Escherichia coli [TaxId:562] [187306] (27 PDB entries)

    6. Species Escherichia coli [TaxId:668369] [189787] (1 PDB entry)

    7. Species Escherichia sp. [TaxId:299586] [188841] (1 PDB entry)

    8. Species Klebsiella oxytoca [TaxId:571] [188743] (1 PDB entry)

    9. Species Klebsiella pneumoniae [TaxId:573] [188184] (2 PDB entries)

    10. Species Oceanobacillus iheyensis [TaxId:182710] [189232] (1 PDB entry)

    11. Species Pneumococcus (Streptococcus pneumoniae) [TaxId:1313] [188417] (2 PDB entries)

    12. Species Staphylococcus aureus [TaxId:1280] [189852] (2 PDB entries)

    13. Species Streptomyces sp. [TaxId:31952] [186885] (1 PDB entry)

More info for Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase

Timeline for Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase:

• Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase first appeared (with stable ids) in SCOP 1.55
  
• Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase appears in SCOP 1.75
  
• Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase appears in SCOPe 2.02
  
• Family e.3.1.1: beta-Lactamase/D-ala carboxypeptidase appears in the current release, SCOPe 2.08