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Crystal structure of Penicillin-Binding Protein 6 (PBP6) from E. coli in complex with a substrate fragment

Source organisms:
Biochemical function: protein homodimerization activity
Biological process: cell wall organization
Cellular component: outer membrane-bounded periplasmic space

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EC 3.4.16.4: Serine-type D-Ala-D-Ala carboxypeptidase

Reaction catalysed:
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Systematic name:
-
Alternative Name(s):
  • D-alanine carboxypeptidase
  • D-alanyl carboxypeptidase
  • D-alanyl-D-alanine carboxypeptidase
  • D-alanyl-D-alanine-carboxypeptidase
  • D-alanyl-D-alanine-cleaving peptidase
  • D-alanyl-D-alanine-cleaving-peptidase
  • DD-carboxypeptidase
  • DD-peptidase
  • DD-transpeptidase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF07943
Domain description: Penicillin-binding protein 5, C-terminal domain
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
The deposited structure of PDB entry 3itb contains 4 copies of Pfam domain PF07943 (Penicillin-binding protein 5, C-terminal domain) in D-alanyl-D-alanine carboxypeptidase DacC. Showing 1 copy in chain D.

PF00768
Domain description: D-alanyl-D-alanine carboxypeptidase
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
The deposited structure of PDB entry 3itb contains 4 copies of Pfam domain PF00768 (D-alanyl-D-alanine carboxypeptidase) in D-alanyl-D-alanine carboxypeptidase DacC. Showing 1 copy in chain D.

InterPro InterPro annotations
IPR018044
Domain description: Peptidase S11, D-alanyl-D-alanine carboxypeptidase A
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
IPR012338
Domain description: Beta-lactamase/transpeptidase-like
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
IPR037167
Domain description: D-Ala-D-Ala carboxypeptidase, C-terminal domain superfamily
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
IPR015956
Domain description: Penicillin-binding protein, C-terminal domain superfamily
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
IPR012907
Domain description: Peptidase S11, D-Ala-D-Ala carboxypeptidase A, C-terminal
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
IPR001967
Domain description: Peptidase S11, D-alanyl-D-alanine carboxypeptidase A, N-terminal
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC

Structure domains

CATH CATH domains
2.60.410.10
Class: Mainly Beta
Architecture: Sandwich
Topology: Peptidoglycan synthesis regulatory factor (PBP3), Domain 2
Homology: D-Ala-D-Ala carboxypeptidase, C-terminal domain
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
The deposited structure of PDB entry 3itb contains 4 copies of CATH domain 2.60.410.10 (Peptidoglycan synthesis regulatory factor (PBP3), Domain 2) in D-alanyl-D-alanine carboxypeptidase DacC. Showing 1 copy in chain D.
3.40.710.10
Class: Alpha Beta
Architecture: 3-Layer(aba) Sandwich
Topology: Beta-lactamase
Homology: DD-peptidase/beta-lactamase superfamily
Occurring in:
  1. D-alanyl-D-alanine carboxypeptidase DacC
The deposited structure of PDB entry 3itb contains 4 copies of CATH domain 3.40.710.10 (Beta-lactamase) in D-alanyl-D-alanine carboxypeptidase DacC. Showing 1 copy in chain D.

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