Family S12
Summary for family S12
| Name | Peptidase family S12 (D-Ala-D-Ala carboxypeptidase B family) |
|---|
| Family type peptidase | S12.001 - D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans), MEROPS Accession MER0000459 (peptidase unit: 32-380) |
| Content of family | Peptidase 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 type | Serine |
| Active site residues | S93 K96 Y190 |
| Active site | The 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 specificities | The 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). |
| Inhibitors | Beta-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 structure | The 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). |
| Clan | SE |
| Basis of clan assignment | Type family of clan SE. |
| Peptidases and Homologues |
MEROPS ID |
Structure |
| D-Ala-D-Ala carboxypeptidase B | S12.001 | Yes |
| aminopeptidase DmpB | S12.002 | Yes |
| alkaline D-peptidase | S12.003 | Yes |
| LACT-1 peptidase | S12.004 | - |
| class C beta-lactamase | S12.006 | Yes |
| Pab87 peptidase | S12.008 | Yes |
| microcystinase MlrB | S12.009 | - |
| colibactin peptidase (Escherichia-type) | S12.010 | Yes |
| XcnG peptidase (Xenorhabdus nematophila) | S12.011 | Yes |
| AmpH protein (Escherichia-type) | S12.012 | Yes |
| paenidase | S12.013 | - |
| esterase EstB | S12.950 | Yes |
| D-amino acid amidase (Ochrobactrum anthropi-type) | S12.951 | Yes |
| ybbE (Bacillus subtilis) | S12.952 | - |
| 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 | - |
| Family S12 non-peptidase homologues | non-peptidase homologue | - |
| Family S12 unassigned peptidases | unassigned | Yes |
