Family M23
Summary for family M23
| Family type peptidase | M23.001 - beta-lytic metallopeptidase (Achromobacter lyticus), MEROPS Accession MER0001281 (peptidase unit: 196-374) |
| Content of family | Peptidase family M23 contains endopeptidases that lyse bacterial cell wall peptidoglycans. |
| History |
Identifier created: Biochem.J. 290:205-218 (1993)
The peptidase from Lysobacter enzymogenes is beta-lytic metalloendopeptidase. The same organism secretes alpha-lytic endopeptidase (S01.268) which is an unrelated serine peptidase. |
| Catalytic type | Metallo |
| Active site | One zinc ion is bound per peptidase molecule, and the zinc ligands have been identified as His227, Asp231 and His318. His316 is a catalytic residue (Odintsov et al., 2004). The active site residues occur in the following motifs: HXXXD and HXH (see the Alignment). |
| Activities and specificities | The peptidases in the family cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase, M23.001) or a bond within the cross-linking peptide (e.g. stapholysin, M23.002, and lysostaphin, M23.004). There is a preference for cleavage of Gly bonds, and because of this, elastin, which is glycine-rich, is often used as a substrate. The pH optima are in the range 8-9. |
| Inhibitors | Lysostaphin is, like many other metallopeptidases, inhibited by metal chelators such as 1,10-phenanthroline and EDTA. |
| Molecular structure | The tertiary structure has been determined for lysostaphin (M23.004) and shows a two-domain beta protein. The larger domain contains the active site and has a six-strand beta-sheet (Odintsov et al., 2004). The vicinity of the active site is similar to that of the zinc D-Ala-D-Ala-carboxypeptidases in family M15 (Bochtler et al., 2004), but the absence of helix forces us to conclude that the structures are not homologous. Consequently, lysostaphin is the type enzyme for clan MO. |
| Clan | MO |
| Basis of clan assignment | For members of this family predicted zinc ligands occur in the motif HXH which is unlike that in any other family. |
| Biological functions | Peptidases of family M23 are used by certain bacteria to lyse cell walls of other bacteria, either as a defensive or feeding mechanism. The soil bacterium Lysobacter enzymogenes is also capable of lysing soil nematodes. The peptidases are synthesized as precursors and are activated extracellularly. Lysostaphin is bound to the cell wall at its C-terminus (Baba & Schneewind, 1996). |
| Statistics for family M23 | Sequences: | 10283 |
| Identifiers: | 18 |
| Identifiers with PDB entries: | 12 |
| Downloadable files |
Sequence library (FastA format) |
| Sequence alignment (FastA format) |
| Phylogenetic tree (Newick format) |
| Peptidases and Homologues |
MEROPS ID |
Structure |
| lysostaphin | M23.004 | Yes |
| zoocin A | M23.005 | Yes |
| enterolysin A | M23.007 | - |
| gp13 peptidase (bacteriophage phi-29) | M23.008 | Yes |
| Mername-AA292 peptidase | M23.009 | Yes |
| LytH peptidase | M23.010 | - |
| YebA peptidase | M23.011 | Yes |
| ALE-1 glycylglycine endopeptidase (Staphylococcus capitis) | M23.012 | Yes |
| LytM glycyl-glycine endopeptidase (Staphylococcus aureus) | M23.013 | Yes |
| ShyA D,D-endopeptidase (Vibrio cholerae) | M23.014 | Yes |
| YibP g.p. (Escherichia sp.) | M23.950 | Yes |
| DipM g.p. (Caulobacter sp.) | M23.951 | - |
| BSSC8_21440 g.p. (Bacillus subtilis) | M23.A03 | - |
| yomI g.p. (Bacillus subtilis) | M23.A04 | - |
| yunA g.p. (Bacillus subtilis) | M23.A06 | - |
| Subfamily M23B non-peptidase homologues | non-peptidase homologue | Yes |
| Subfamily M23B unassigned peptidases | unassigned | Yes |
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Peptidases not assigned to subfamily
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