Summary for clan SE

Summary Alignment Structure Literature
Clan type peptidaseS12.001 - D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans), MEROPS Accession MER0000459 (peptidase unit: 32-380); PDB accession 3PTE
HistoryBiochem.J. 290:205-218 (1993)
DescriptionSerine nucleophile; catalytic residues in the order Ser, Lys (within the motif SXXK) in sequence
Contents of clanClan SE contains peptidases specialised for roles in bacterial cell wall metabolism.
EvidenceThe homology of families S11, S12 and S13 is supported by similarities in sequence, protein fold, catalytic mechanism and biological functions.
Catalytic mechanismThere 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 activityMost 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 foldTertiary 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 familiesMany 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 PFAMCL0013
SCOP56601

Families

Family Family Type Peptidase Structure
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

FamilyBacteriaArchaeaProtozoaFungiPlantsAnimalsViruses
S11+++++++
S12+++++++
S13++++++-
Clan+++++++