Family S11

Family

Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family S11

NamePeptidase family S11 (D-Ala-D-Ala carboxypeptidase A family)
Family type peptidaseS11.001 - D-Ala-D-Ala carboxypeptidase A (Geobacillus stearothermophilus), MEROPS Accession MER0000448 (peptidase unit: 31-452)
Content of familyPeptidase family S11 contains serine-type D-Ala-D-Ala carboxypeptidases.
History Identifier created: Biochem.J. 290:205-218 (1993)
Catalytic typeSerine
Active site residuesS66 K69 S130 
Active siteThe active site residues Ser and Lys form the catalytic dyad and are found in the motif Ser-Xaa-Thr-Lys. There is a further catalytic Ser residue further toward the C-terminus in a conserved Ser-Xaa-Asn motif.
Activities and specificitiesTwo main types of enzymatic activity are found in family S11. These are 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. There are peptidases that have both activities.
InhibitorsAntibiotics of the beta-lactam family inactivate some members of family S11 through acylation of the active site serine.
Molecular structureFamily S11 is included in clan SE as the protein fold of the peptidase unit for members of this family resembles that of the type example of family S12, D-Ala-D-Ala-carboxypeptidase B (S12.001). The peptidases of family S11 contain two domains - one of alpha helices and one containing an alpha-beta sandwich. The active site residues reside on a helix that crosses the cleft between the two lobes. The all-alpha helix domain, containing the third catalytic residue in the motif Ser-Xaa-Asn, forms one side of the cavity whereas the other side is formed by the third strand of the beta sheet containing a Lys-Thr-Gly motif.
ClanSE
Basis of clan assignmentProtein fold of the peptidase unit for members of this family resembles that of D-Ala-D-Ala-carboxypeptidase B, the type example for clan SE.
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi -  
Plants details  
Animals details  
Viruses details  
Biological functionsThe peptidases of family S11 are mainly involved in the synthesis of bacterial cell walls, cleaving the D-Ala-D-Ala crosslinks in the cell wall peptidoglycans. Many of the enzymes are also penicillin-binding proteins (PBPs).
Statistics for family S11Sequences:12907
Identifiers:11
Identifiers with PDB entries:6
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Other databases CATH 3.40.710.10
INTERPRO IPR001967
PANTHER PTHR21581
PFAM PF00144
PFAM PF00768
PFAM PF13354
SCOP 56602
Peptidases and Homologues MEROPS ID Structure
D-Ala-D-Ala carboxypeptidase AS11.001-
murein-DD-endopeptidaseS11.002-
penicillin-binding protein 6S11.003Yes
K15-type DD-transpeptidaseS11.004Yes
D-Ala-D-Ala carboxypeptidase DacFS11.005-
D,D-carboxypeptidase PBP3 (Streptococcus-type)S11.006Yes
penicillin-binding protein 4 (Neisseria)-type peptidaseS11.007-
penicillin-binding protein 5-type peptidaseS11.008Yes
penicillin-binding protein 6b-type peptidaseS11.009-
penicillin-binding protein 4 (Staphylococcus)-type peptidaseS11.010Yes
penP g.p. (Bacillus subtilis)S11.A01-
family S11 non-peptidase homologuesnon-peptidase homologue-
family S11 unassigned peptidasesunassignedYes