Family C40
Summary for family C40
| Family type peptidase | C40.001 - dipeptidyl-peptidase VI (bacteria) (Lysinibacillus sphaericus), MEROPS Accession MER0001322 (peptidase unit: 154-271) |
| Content of family | Peptidase family C40 contains bacterial cell-wall modifying enzymes. |
| History |
Identifier created: Proteolysis in Cell Function, pp13-21, IOS Press, Amsterdam (1997)
|
| Catalytic type | Cysteine |
| Active site residues | C178 H224 E,H,N,Q236 |
| Active site | The peptidase units of dipeptidylpeptidase VI (DPP VI; C40.001) and the other proteins assigned to family C40 are the C-terminal 110-residue segments of the proteins. These contain single conserved cysteine and histidine residues that form a catalytic triad in the order Cys, His, His (see the Alignment). These were confirmed from the solution structure of the spr gene product from Escherichia coli (Aramini et al., 2008). A catalytic triad with two histidines is also found in serine peptidases from clan SH.
On the basis of Psi-BLAST searches starting from peptidases of family C40, Anantharaman & Aravind, 2003 described the 'NlpC/P60 superfamily' of proteins. |
| Activities and specificities | DPP VI hydrolyses substrates of the general structure L-Ala-gamma-D-Glu L-Zaa-Yaa, in which Zaa is a di-amino acid such as L-lysine or diaminopimelic acid, and Yaa is D-Ala or D-Ala-D-Ala. Activity is stimulated by 5 mM EDTA and 1 mM DTT. |
| Inhibitors | DPP VI is inhibited by N-ethylmaleimide, iodoacetamide and phydroxymercuribenzoate. |
| Molecular structure | The tertiary structures of the gene products spr from Escherichia coli (Aramini et al., 2008), Ava_3396 from Anabaena variabilis and Npun0240 from Nostoc punctiforme (both unpublished) have been solved. All show structures reminiscent of the papain fold, with two subdomains, one consisting of a helical bundle and which bears the catalytic Cys, the other a beta barrel bearing the other active site residues. Unlike papain, where the catalytic Cys is at the N-terminus of a helix, in the structures from family C40 the active site Cys is at the C-terminus of a helix, which means the sequence must run in the opposite direction to that in papain. No similarity between the structures can be detected using the DALI algorithm (Holm & Sander, 1995). The structural resemblances are therefore assumed to be derived from convergent rather than divergent evolution, and proteins in C40 are assigned to the clan CO. All members of this family have either a signal peptide or a transmembrane region, indicating a cell-surface location. |
| Clan | CO |
| Basis of clan assignment | Type family of clan CO. |
| Peptidases and Homologues |
MEROPS ID |
Structure |
| dipeptidyl-peptidase VI (bacteria) | C40.001 | - |
| murein peptidase LytF | C40.002 | - |
| murein peptidase lytE | C40.003 | - |
| spr peptidase | C40.004 | Yes |
| PgdS peptidase | C40.005 | - |
| PgpA peptidase | C40.006 | - |
| YddH peptidase | C40.007 | Yes |
| CwlS peptidase (Bacillus sp.) | C40.008 | - |
| NLP/P60 (Nostoc punctiforme)-like putative peptidase | C40.009 | Yes |
| CwlO peptidase (Bacillus sp.) | C40.010 | - |
| RipA peptidoglycan hydrolase | C40.011 | - |
| RipB peptidoglycan hydrolase | C40.012 | Yes |
| YdhO protein (Escherichia coli) | C40.013 | - |
| BacL1 peptidase (Enterococcus faecalis) | C40.014 | - |
| LytFM (Dermatophagoides pteronyssinus) | C40.015 | - |
| NlpC protein (Escherichia coli) | C40.A01 | - |
| I33_2179 protein (Bacillus subtilis) | C40.A06 | - |
| I33_1064 protein (Bacillus subtilis) | C40.A07 | - |
| I33_1070 protein (Bacillus subtilis) | C40.A08 | - |
| BSSC8_33880 (Bacillus subtilis) | C40.A09 | - |
| phosphatase-associated protein (Bacillus subtilis) | C40.A10 | - |
| Family C40 non-peptidase homologues | non-peptidase homologue | - |
| Family C40 unassigned peptidases | unassigned | Yes |
