Summary for clan ME
Clan type peptidase | M16.003 - mitochondrial processing peptidase beta-subunit (Saccharomyces cerevisiae), MEROPS Accession MER0001229 (peptidase unit: 30-245); PDB accession 1HR6_B |
History | PEPTIDAS.TXT (SwissProt document) |
Description | Water nucleophile; water bound by single zinc ion ligated to two His (within the motif HXXEH) and Glu |
Contents of clan | Clan ME contains two families in which two of the zinc ligands occur in the motif His-Xaa-Xaa-Glu-His ("HXXEH"). |
Evidence | Both 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 mechanism | The 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 activity | The peptidases in clan ME have varied endopeptidase specificities. |
Protein fold | The 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 families | A similar fold is found in the autoinducer-2 production protein LuxS (Ruzheinikov et al., 2001). |
Activation mechanism | All of the peptidases in clan ME are metal-dependence. |
Other databases
| PFAM | CL0094 |
| SCOP | 63411 |
Families
M16 |
pitrilysin (Escherichia coli) |
Yes |
M44 |
pox virus metallopeptidase (Vaccinia virus) |
- |
Distribution of clan ME among Kingdoms of Organisms
M16 | - | - | - | - | - | - | - |
M44 | - | - | - | - | - | - | - |
Clan | - | - | - | - | - | - | - |