Summary for clan ME

Summary Alignment Structure Literature
Clan type peptidaseM16.003 - mitochondrial processing peptidase beta-subunit (Saccharomyces cerevisiae), MEROPS Accession MER0001229 (peptidase unit: 30-245); PDB accession 1HR6_B
HistoryPEPTIDAS.TXT (SwissProt document)
DescriptionWater nucleophile; water bound by single zinc ion ligated to two His (within the motif HXXEH) and Glu
Contents of clanClan ME contains two families in which two of the zinc ligands occur in the motif His-Xaa-Xaa-Glu-His ("HXXEH").
EvidenceBoth families have active site residues His, Glu, His, Glu, Glu, of which three are zinc ligands and two are catalytic Glu residues (see the Alignment).
Catalytic mechanismThe His residues and the Glu C-terminal to the motif HXXEH have been shown to be zinc ligands in pitrilysin (M16.001), the type example of family M16. Glu in the HXXEH motif is important for catalysis (Becker et al., 1992).
Peptidase activityThe peptidases in clan ME have varied endopeptidase specificities.
Protein foldThe first tertiary structures to be determined were from the non-peptidase homologue that is part of the cytochrome bc1 complex (Xia et al., 1997); subsequently the structure of the mitochondrial processing peptidase has been determined (M16.003; Taylor et al., 2001). Peptidases in the subfamily M16B have a fold containing two domains derived from an ancient gene duplication event. Each domain contains a six strand beta sheet and a bundle of six helices in two layers. Only the N-terminal domain carries an active site. No tertiary structure has been published for any member of subfamily M16A, but two peptidase units are present, with the active site restricted to the N-terminal domain. Proteins in subfamily M16A are twice as long as those in subfamily M16B, so it is possible that two duplication events have occurred and that four peptidase units are present, but that three are no longer functional and two have diverged so much that they are no longer detectable in sequence comparisons.
Homologous non-peptidase familiesA similar fold is found in the autoinducer-2 production protein LuxS (Ruzheinikov et al., 2001).
Activation mechanismAll of the peptidases in clan ME are metal-dependence.
Other databases PFAMCL0094


Family Family Type Peptidase Structure
M16 pitrilysin (Escherichia coli) Yes
M44 pox virus metallopeptidase (Vaccinia virus) -

Distribution of clan ME among Kingdoms of Organisms