Family M55


Summary Holotypes Alignment Tree Genomes Structure Literature

Summary for family M55

NamePeptidase family M55 (DppA aminopeptidase family)
Family type peptidaseM55.001 - D-aminopeptidase DppA (Bacillus subtilis), MEROPS Accession MER0005922 (peptidase unit: 1-274)
Content of familyPeptidase family M55 contains an aminopeptidase and a number of uncharacterised putative peptidases.
History Identifier created: MEROPS 5.4 (23 March 2001)
A peptidase that hydrolyses D-Ala-D-Ala and D-Ala-Gly-Gly was discovered in several species of Bacillus and termed DppA (Cheggour et al., 2000).
Catalytic typeMetallo
Active site residuesD8 E10 H60 H104 H115 E133 
Active siteThe catalytic residue and five metal ligands are conserved throughout the family, as is the SXDXEG motif containing the first two metal ligands near to the N-terminus (see the Alignment). One of the zinc atoms is bound by Asp8, Glu10 and His60, and the other by Asp8, His104 and Glu133 (Remaut & Goffin, 2004). The significance of the occurrence of an active site His in DppA where Glu might have been expected in other co-catalytic metallopeptidases has been investigated (Bzymek et al., 2005).
Activities and specificitiesThe best known substrates are D-Ala-D-Ala and D-Ala-Gly-Gly (Remaut & Goffin, 2004).
InhibitorsDppA is inhibited by zinc chelators.
Molecular structureThe crystal structure of DppA has been solved (Remaut et al., 2001). The DppA complex is a homodecamer with the subunits in a barrel arrangement forming a central chamber. Each monomeric subunit contains two distinct domains. The N-terminal domain contains a six-stranded beta-sheet which is flanked by two alpha-helices on each side and is responsible for the formation of the active site (Remaut & Goffin, 2004). The smaller C-terminal domain consists of a five-stranded antiparallel beta-sheet which is flanked by one alpha-helix on each side. This domain is responsible for the oligomerization of the enzyme (Remaut & Goffin, 2004). It has been pointed out that the structure of the complex is reminiscent of those of so called 'self-compartmentalizing' peptidases that create an internal compartment in which the active sites are located (Remaut et al., 2001). Self-compartmentalizing peptidases include the proteasomes in family T1 and Clp peptidases in family S14 (Lupas et al., 1997).
Basis of clan assignmentType family of clan MN.
Distribution of family Bacteria details  
Archaea details  
Protozoa -  
Fungi -  
Plants -  
Animals details  
Viruses -  
Biological functionsThe role of DppA in Bacillus subtilis is thought to be as an adaptation to nutrient deficiency. Following hydrolysis of (D-Ala)2, the released D-Ala could be used as a metabolic fuel (Remaut & Goffin, 2004).
Statistics for family M55Sequences:758
Identifiers with PDB entries:1
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Peptidases and Homologues MEROPS ID Structure
D-aminopeptidase DppAM55.001Yes
PF1591 g.p. (Pyrococcus furiosus)M55.A01-
family M55 non-peptidase homologuesnon-peptidase homologue-
family M55 unassigned peptidasesunassigned-