Family S13


Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family S13

NamePeptidase family S13 (D-Ala-D-Ala peptidase C family)
Family type peptidaseS13.001 - D-Ala-D-Ala peptidase C (Escherichia coli), MEROPS Accession MER0000472 (peptidase unit: 21-477)
Content of familyThe family contains peptidases that cleave D-Ala bonds, acting either as carboxypeptidases or as atypical 'endopeptidases'.
History Identifier created: Biochem.J. 290:205-218 (1993)
Catalytic typeSerine
Active site residuesS62 K65 S306 
Active siteCatalysis depends upon a Ser/Lys dyad in which the serine carries the nucleophile and the lysine acts as the general base. These residues occur in the motif -Ala-Ser-Xaa-Xaa-Lys-Xbb-, in which Xaa is an uncharged amino acid and Xbb is an aliphatic, hydrophobic amino acid. A similar SXXK motif occurs in families S11 and S12. A third residue is important for activity: the serine in the motif -Ser-Xcc-Asn-, in which Xcc is usually Asp or Asn.
Activities and specificitiesPenicillin-binding protein 4 (PBP4, S13.001) hydrolyses the D-AlaD-Ala bond in the cross-linking peptide precursor, and performs the transpeptidation reaction between the D-Ala and the meso-2,6-diaminopimelate of adjacent crosslinking peptides of the bacterial cell wall. It also degrades this D-Alameso-2,6-diaminopimelate bond in what has been called an 'endopeptidase' reaction, although the bond cleaved is not a standard alpha-carbon-nitrogen bond. The D-Ala-D-Ala carboxypeptidase from Actinomadura (S13.002) does not perform the endopeptidase reaction. Maximum activity is seen between pH 8 and 9 (Wilkin, 2004).
InhibitorsAntibiotics containing a beta-lactam, including penicillins and cephalosporins, inactivate the enzymes by acylating the active site serine, but there is no interaction at the P1 site.
Molecular structureOnly preliminary crystallographic data have been obtained so far. The peptidases in this family have a greater molecular mass than peptidases in the related families S11 and S12, and it has been proposed that this is because of a large insert between the SXXK and SXN motifs (Thunnissen et al., 1995).
Basis of clan assignmentPredicted active site residues for members of this family and family S12 occur in the motif SXXK.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi -  
Plants details  
Animals details  
Viruses -  
Biological functionsPBP4 is periplasmic, loosely attached to the membrane. It is important both in the biosynthesis and turnover of the bacterial cell wall crosslinks; it is, however, not essential and deletion mutants are able to grow normally (Wilkin, 2004).
Statistics for family S13Sequences:2931
Identifiers with PDB entries:2
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Other databases INTERPRO IPR000667
PFAM PF02113
SCOP 144046
Peptidases and Homologues MEROPS ID Structure
D-Ala-D-Ala peptidase CS13.001Yes
D-Ala-D-Ala carboxypeptidase (Actinomadura-type)S13.002Yes
D-Ala-D-Ala carboxypeptidase PBP3S13.003-
penillin-binding protein 4S13.004-
Bd3459 D-alanyl-D-alanine carboxypeptidase (Bdellovibrio bacteriovorus)S13.005-
pscA g.p. (Dictyostelium discoideum)S13.A01-
family S13 non-peptidase homologuesnon-peptidase homologue-
family S13 unassigned peptidasesunassigned-