Summary for clan SE
Clan type peptidase | S12.001 - D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans), MEROPS Accession MER0000459 (peptidase unit: 32-380); PDB accession 3PTE |
History | Biochem.J. 290:205-218 (1993) |
Description | Serine nucleophile; catalytic residues in the order Ser, Lys (within the motif SXXK) in sequence |
Contents of clan | Clan SE contains peptidases specialised for roles in bacterial cell wall metabolism. |
Evidence | The homology of families S11, S12 and S13 is supported by similarities in sequence, protein fold, catalytic mechanism and biological functions. |
Catalytic mechanism | There is a closely-spaced catalytic dyad Ser66, Lys69. A third residue, Ser/Tyr130, also plays a part in catalysis (Rhazi et al., 2003). These active site residues are contained in conserved motifs Ser-Xaa-Xaa-Lys (in all three families) and Ser-Xaa-Asn (in most members of S11 and S13; in S12 the Ser is replaced by Tyr: see the family Alignments). |
Peptidase activity | Most of the peptidases in the family are carboxypeptidases, but there is also at least one aminopeptidase as well as enzymes that are termed "endopeptidases" because of the way they cleave bonds in bacterial cell wall although they do not hydrolyse alpha-peptide bonds. |
Protein fold | Tertiary structures have been determined and shown to be similar for members of families S11 (Englebert et al., 1994), S12 (Kelly et al., 1985) and S13 (Sauvage et al., 2005). Peptidases in clan SE have two structural domains, an N-terminal helical bundle and a C-terminal alpha/beta/alpha sandwich. The active site is located within the N-terminal domain with the SXXK motif on one helix and the SXN motif on another. Peptidases in family S13 have two additional domains inserted between the active site motifs and lack the C-terminal domain (Sauvage et al., 2005). |
Homologous non-peptidase families | Many other penicillin-binding proteins, as well as glutaminases from Bacillus subtilis and Escherichia coli, have been shown to have similar structures. Tertiary structures are also known for beta-lactamases of classes A, B and C, which are non-peptidase homologues of family S12. |
Other databases
| PFAM | CL0013 |
| SCOP | 56601 |
Families
S11 |
D-Ala-D-Ala carboxypeptidase A (Geobacillus stearothermophilus) |
Yes |
S12 |
D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans) |
Yes |
S13 |
D-Ala-D-Ala peptidase C (Escherichia coli) |
Yes |
Distribution of clan SE among Kingdoms of Organisms