Family S12


Summary Holotypes Alignment Tree Genomes Structure Literature H-seq M-seq

Summary for family S12

NamePeptidase family S12 (D-Ala-D-Ala carboxypeptidase B family)
Family type peptidaseS12.001 - D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans), MEROPS Accession MER0000459 (peptidase unit: 32-380)
Content of familyPeptidase family S12 contains serine-type D-Ala-D-Ala carboxypeptidases.
History Identifier created: Biochem.J. 290:205-218 (1993)
D-Ala-D-Ala carboxypeptidase B has been reviewed by Frere (2004).
Catalytic typeSerine
Active site residuesS93 K96 Y190 
Active siteThe active site residues Ser and Lys form the catalytic dyad and are found in the motif Ser-Xaa-Thr-Lys (see the Alignment). There is a catalytic Tyr residue further toward the C-terminus in a conserved Tyr-Xaa-Asn motif. The tyrosine is replaced by serine in other families of clan SE.
Activities and specificitiesThe peptidases of family S12 exhibit a wide range of activities and specificities. D-Ala-D-Ala carboxypeptidase B (S12.001) catalyses two reactions: DD-carboxypeptidase activity in which there is transfer of the C-terminal D-Ala to water, and DD-transpeptidase activity in which the peptidoglycan monomer is transferred to an exogenous receptor after removal of the C-terminal D-Ala. The C-terminal D-Ala can be replaced by Gly, D-Lys, D-Leu, or D-Glu which will be cleaved at 10% the normal efficiency (Frère, 2004). Aminopeptidase DmpB (S12.002) hydrolyses Gly-NH2 and D-Ser-NH2 at 44% and 29% of the normal efficiency of D-Ala-NH2 (Asano, 2004). Alkaline D-peptidase (S12.003) converts (D-Phe)4 and (D-Phe)3 to (D-Phe)2 and D-Phe (Asano, 2004).
InhibitorsBeta-lactam compounds inhibit members of family S12, and a highly specific tripeptide phosphonate inhibitor of D-Ala-D-Ala carboxypeptidase B has also been described (Silvaggi et al., 2003).
Molecular structureThe structure of the type example of family S12, D-Ala-D-Ala carboxypeptidase B (S12.001), was solved by Kelly et al., 1986. The active peptidase is 349 residues in length and is composed of two domains, one of which consists of all alpha helices and the second of a mixture of alpha helices and beta structures. The active site is found at the interface of the two domains. The precursor contains a 31-residue signal peptide and a 26-residue C-terminal extension (Duez et al., 1987; Joris et al., 1987).
Basis of clan assignmentType family of clan SE.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi -  
Plants details  
Animals details  
Viruses details  
Biological functionsD-Ala-D-Ala carboxypeptidase B is involved in the synthesis and remodelling of bacterial cell walls.
Statistics for family S12Sequences:24279
Identifiers with PDB entries:9
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Other databases CATH 3.40.710.10
PFAM PF00144
SCOP 56602
Peptidases and Homologues MEROPS ID Structure
D-Ala-D-Ala carboxypeptidase BS12.001Yes
aminopeptidase DmpBS12.002Yes
alkaline D-peptidaseS12.003Yes
LACT-1 peptidaseS12.004-
class C beta-lactamaseS12.006Yes
Pab87 peptidaseS12.008Yes
microcystinase MlrBS12.009-
colibactin peptidase (Escherichia-type)S12.010Yes
XcnG peptidase (Xenorhabdus nematophila)S12.011-
AmpH protein (Escherichia-type)S12.012-
esterase EstBS12.950Yes
D-amino acid amidase (Ochrobactrum anthropi-type)S12.951Yes
At5g24810 (Arabidopsis thaliana)S12.A01-
EcHS_A2566 protein (Escherichia coli)S12.A03-
lact-6 g.p. (Caenorhabditis elegans)S12.A09-
lact-5 g.p. (Caenorhabditis elegans)S12.A10-
lact-2 g.p. (Caenorhabditis elegans)S12.A11-
lact-8 g.p. (Caenorhabditis elegans)S12.A12-
lact-7 g.p. (Caenorhabditis elegans)S12.A13-
lact-3 g.p. (Caenorhabditis elegans)S12.A14-
lact-1 g.p. (Caenorhabditis elegans)S12.A15-
lact-9 g.p. (Caenorhabditis elegans)S12.A16-
lact-4 g.p. (Caenorhabditis elegans)S12.A17-
pbpX g.p. (Bacillus subtilis)S12.A21-
BSU6633_13517 g.p. (Bacillus subtilis)S12.A22-
GYO_0385 g.p. (Bacillus subtilis)S12.A23-
DDB_G0282557 g.p. (Dictyostelium discoideum)S12.A24-
DDB_G0282555 g.p. (Dictyostelium discoideum)S12.A25-
DDB_G0275107 g.p. (Dictyostelium discoideum)S12.A26-
DDB_G0294597 g.p. (Dictyostelium discoideum)S12.A27-
pksF (Bacillus subtilis)S12.A28-
ybbE (Bacillus subtilis)S12.A29-
family S12 non-peptidase homologuesnon-peptidase homologue-
family S12 unassigned peptidasesunassignedYes