Conserved Protein Domain Family

cd12797: M23_peptidase 
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins
This model describes the metallopeptidase M23 family, which includes beta-lytic metallopeptidase and lysostaphin. Members of this family are zinc endopeptidases that lyse bacterial cell wall peptidoglycans; they cleave either the N-acylmuramoyl-Ala bond between the cell wall peptidoglycan and the cross-linking peptide (e.g. beta-lytic endopeptidase) or a bond within the cross-linking peptide (e.g. stapholysin, and lysostaphin). Beta-lytic metallopeptidase, formerly known as beta-lytic protease, has a preference for cleavage of Gly-X bonds and favors hydrophobic or apolar residues on either side. It inhibits growth of sensitive organisms and may potentially serve as an antimicrobial agent. Lysostaphin, produced by Staphylococcus genus, cleaves pentaglycine cross-bridges of cell wall peptidoglycan, acting as autolysins to maintain cell wall metabolism or as toxins and weapons against competing strains. Staphylolysin (also known as LasA) is implicated in a range of processes related to Pseudomonas virulence, including stimulating shedding of the ectodomain of cell surface heparan sulphate proteoglycan syndecan-1, and elastin degradation in connective tissue. Its active site is less constricted and contains a five-coordinate zinc ion with trigonal bipyramidal geometry and two metal-bound water molecules, possibly contributing to its activity against a wider range of substrates than those used by related lytic enzymes, consistent with its multiple roles in Pseudomonas virulence. The family includes members that do not appear to have the conserved zinc-binding site and might be lipoproteins lacking proteolytic activity.
PSSM-Id: 410984
Aligned: 604 rows
Threshold Bit Score: 42.5789
Created: 22-Feb-2011
Updated: 25-Oct-2021
Aligned Rows:
active site
Conserved site includes 4 residues -Click on image for an interactive view with Cn3D
Feature 1: active site [active site], 4 residue positions
Conserved feature residue pattern:H D H HClick to see conserved feature residue pattern help
  • Comment:active site residues occur in HXXXD and HXH motifs
  • Structure:2B13: Staphylococcus aureus glycyl-glycine endopeptidase LytM binds zinc and tartrate molecule; contacts at 4A
    View structure with Cn3D
  • Comment:tartrate molecule from the buffer is found in the active site of LytM and is in contact with the zinc ion via the carboxylate group
  • Structure:4QP5: Staphylococcus simulans lysostaphin binds zinc ion and a phosphate ion in the active site; contacts at 4A
    View structure with Cn3D

Sequence Alignment
Format: Row Display: Color Bits: Type Selection:
Feature 1         #   #                                                                           
2B13_A         28 HYGVDYam-----peNSPVYSLt--DGTVVQAgwsny-------------gggnQVTIKEans---------nnYQWYMH 78   Staphylococcu...
EDN69833      195 HLGYDIyv------nQNNVIAAa--DGFVHKVrksr--------------maglYVKLHHgn----------qlYTLYIH 242  Beggiatoa sp. PS
EGV50453      125 HKGIDIpq-----prGTPVRAIa--NGVVVGKflnef------------nrkgiEIILRHtpeqtg---lpfwtYSQYTH 182  endosymbiont ...
EGI77796      197 HGGMDMpa-----awDTPILAAa--DGTVVGMygadn------------sqrgrEIVLRHapedtg---lpvwlYTQYAH 254  Hylemonella g...
EKD25639      328 HVGIQIka-----gqWTPVYAAr--DGIVYFVadnde-------------iginRAMIVHtd----------gyVTIYQY 377  uncultured ba...
EKE10745      105 HTGTDFeafsdelekDVPVKAIc--RGKILRKekas---------------gygGVLVEScefg------repiTVVYGH 161  uncultured ba...
EIR36652       42 HGGIHIpht---dsgGTPEKIRaiaDGTVHSLrqpvgdkkgippynyngatdcgYVLLKHeteigsgenakvvyFSLYMH 118  Yersinia pest...
AGA31021      861 HSGLDIgga----egLVDVVAAt--DGFVASAgttltpgfdd---tparprydvVYLVDDrg-----------wFYRYSH 920  Singulisphaer...
EKD76330       98 HTGDDIevtd--vtaEVPFFSLa--DATVLKKeivs--------------gyggVIILEFvdgl-------tvyHALYGH 152  uncultured ba...
WP_014959881  187 HLGEDIda-----peGTPVLAAn--DGKVVLAgrfy--------------ydgnMVIVDHgg----------glFTEYLH 235  Leptospirillu...
Feature 1                                                    # #   
2B13_A         79 n--NRLTVSa--GDKVKAgDQIAYSGStgn---------staPHVHFQR 114  Staphylococcus aureus
EDN69833      243 l--KKANVKv--GQKVRRgDVIGKIDGpvgn--------aiaPQLHFEI 279  Beggiatoa sp. PS
EGV50453      183 l-qEMPTLSi--GTNVKMgDEIGKTANtgkmg-----rrvrrDALHFAV 223  endosymbiont of Riftia pachyptila (vent Ph05)
EGI77796      255 l-nQAPTLKl--GQRVRMgDLVGLTGNsglsaqgdrpttgrrPAIHYAA 300  Hylemonella gracilis ATCC 19624
EKD25639      378 l--KKTVIKp--GDTVRRgQIIWYSWWepgtrga--gfiskgANLTFEI 420  uncultured bacterium (gcode 4)
EKE10745      162 ldlASISKKv--GDNLEAsESIGNLGKnksae-----tdgerKHLHLGI 203  uncultured bacterium
EIR36652      119 lasIDAAVKt--GEKIYRkDPIGTVGQvd-----------ggNAVHFQI 154  Yersinia pestis PY-10
AGA31021      921 l--QSIDPAitpGASVRKgQKIGVLGKegas--------ggwSHLHFEI 959  Singulisphaera acidiphila DSM 18658
EKD76330      153 vdlNSITMVv--GDKVTAgEQLGMLGDdgsse-----adgerKHLHFAI 194  uncultured bacterium
WP_014959881  236 l--RDIRVHp--GERVRCgDLVGHLGHtgr---------vtgPVFHYGA 271  Leptospirillum ferriphilum

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