Family M23

Family

Summary Holotypes Alignment Tree Genomes Structure Literature

M23A

Summary Holotypes Alignment Tree Genomes Literature

M23B

Summary Holotypes Alignment Tree Genomes Literature

Summary for family M23

Family type peptidaseM23.001 - beta-lytic metallopeptidase (Achromobacter lyticus), MEROPS Accession MER0001281 (peptidase unit: 196-374)
Content of familyPeptidase 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 typeMetallo
Active siteOne 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 specificitiesThe 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.
InhibitorsLysostaphin is, like many other metallopeptidases, inhibited by metal chelators such as 1,10-phenanthroline and EDTA.
Molecular structureThe 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.
ClanMO
Basis of clan assignmentFor members of this family predicted zinc ligands occur in the motif HXH which is unlike that in any other family.
Distribution of family Bacteria details  
Archaea details  
Protozoa -  
Fungi details  
Plants details  
Animals details  
Viruses details  
Biological functionsPeptidases 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 M23Sequences:10379
Identifiers:18
Identifiers with PDB entries:9
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Subfamily M23A
Name Peptidase subfamily M23A
Subfamily type peptidase M23.001 - beta-lytic metallopeptidase (Achromobacter lyticus), MEROPS Accession MER0001281 (peptidase unit: 196-374)
Active site residues H217 D231 H316 H318 
Statistics Sequences: 78
Identifiers: 3
Identifiers with PDB entries: 1
Other databases INTERPRO IPR000841
PFAM PF01551
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
beta-lytic metallopeptidaseM23.001-
staphylolysinM23.002Yes
Mername-AA291 peptidaseM23.003-
subfamily M23A unassigned peptidasesnon-peptidase homologue-
subfamily M23A unassigned peptidasesunassigned-
Subfamily M23B
Name Peptidase subfamily M23B
Subfamily type peptidase M23.004 - lysostaphin (Staphylococcus simulans), MEROPS Accession MER0001419 (peptidase unit: 248-390)
Active site residues H279 D283 H360 H362 
Statistics Sequences: 10268
Identifiers: 15
Identifiers with PDB entries: 8
Other databases INTERPRO IPR002886
PANTHER PTHR21666
PFAM PF01551
SCOP 102006
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
lysostaphinM23.004Yes
zoocin AM23.005Yes
enterolysin AM23.007-
gp13 peptidase (bacteriophage phi-29)M23.008Yes
Mername-AA292 peptidaseM23.009-
LytH peptidaseM23.010-
YebA peptidaseM23.011-
ALE-1 glycylglycine endopeptidase (Staphylococcus capitis)M23.012Yes
LytM glycyl-glycine endopeptidase (Staphylococcus aureus)M23.013Yes
ShyA D,D-endopeptidase (Vibrio cholerae)M23.014Yes
YibP g.p. (Escherichia sp.)M23.950-
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 homologuesnon-peptidase homologueYes
subfamily M23B unassigned peptidasesunassignedYes
Peptidases not assigned to subfamily
Peptidases and Homologues MEROPS ID Structure
family M23 non-peptidase homologuesnon-peptidase homologue-
family M23 unassigned peptidasesunassigned-