Family S66

Family

Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family S66

Family type peptidaseS66.001 - murein tetrapeptidase LD-carboxypeptidase (Pseudomonas-type) (Pseudomonas aeruginosa), MEROPS Accession MER0016191 (peptidase unit: 15-307)
Content of familyPeptidase family S66 contains bacterial LD-carboxypeptidases.
History Identifier created: Merops 7.2 (14 October 2005)
Among the first descriptions of LD-carboxypeptidase (S66.002) was the study of Izaki & Strominger (1968) in which the enzyme was termed D-alanine carboxypeptidase II. The enzyme was purified by Ursinus et al. (1992), and the catalytic mechanism and structure were determined for the Pseudomonas enzyme (S66.001) by Korza & Bochtler (2005).
Catalytic typeSerine
Active site residuesS115 E217 H285 
Active siteThere is a catalytic triad, Ser, His Glu (Korza & Bochtler, 2005: see the Alignment). Family S51 also has this triad, but has an unrelated fold.
Activities and specificitiesThe physiological substrates are tetrapeptide peptidoglycan fragments that contain an L-configured residue (lysine or meso-diaminopimelic acid) to which is attached a C-terminal D-alanine residue. It is the bond to the C-terminal D-Ala residue that is hydrolysed.
InhibitorsResults of inhibition studies have been inconsistent (Templin & Holtje, 2004). LD-Carboxypeptidase is notably not inhibited by EDTA or penicillin, unlike some other peptidases with related activities.
Molecular structureThe structure of LD-carboxypeptidase from Pseudomonas aruginosa described by Korza & Bochtler (2005) shows an N-terminal sheet and a C-terminal barrel domain. At the interface of the two domains, the catalytic serine residue adopts a highly strained conformation reminiscent of the 'nucleophilic elbow' in alpha/beta-hydrolases (clan SC).
ClanSS
Distribution of family Bacteria details  
Archaea details  
Protozoa details  
Fungi details  
Plants details  
Animals details  
Viruses -  
Biological functionsLD-carboxypeptidase substrates are produced when bacterial cell walls are degraded, and it is thought that the LD-carboxypeptidase is required to allow murein tetrapeptide fragments to be reincorporated into murein. The tetrapeptides are truncated to the tripeptides, which can then be reconverted into peptidoglycan building blocks by the attachment of preformed D-Ala-D-Ala dipeptides (Korza & Bochtler, 2005). A second member of family S66 in Escherichia coli is the mccF gene product (S66.003) that contributes to self-immunity to microcin C7 (Gonzalez-Pastor et al., 1995).
ReviewsTemplin & Holtje (2004); Korza & Bochtler (2005)
Statistics for family S66Sequences:3669
Identifiers:3
Identifiers with PDB entries:3
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
murein tetrapeptidase LD-carboxypeptidase (Pseudomonas-type)S66.001Yes
murein tetrapeptidase LD-carboxypeptidase (Escherichia-type)S66.002-
microcin C7 immunity proteinS66.003Yes
family S66 non-peptidase homologuesnon-peptidase homologue-
family S66 unassigned peptidasesunassignedYes