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Conserved domains on  [gi|499427839|ref|WP_011115303|]
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M23 family metallopeptidase [Helicobacter hepaticus]

Protein Classification

M23 family metallopeptidase( domain architecture ID 13411669)

M23 family metallopeptidase is an endopeptidase that lyses bacterial cell wall peptidoglycans; also contains an uncharacterized N-terminal domain related to peptidoglycan hydrolase

EC:  3.4.-.-
Gene Ontology:  GO:0008270|GO:0016787|GO:0004222
MEROPS:  M23
PubMed:  10493853|7674922

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 136-221 2.25e-18

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 81.17  E-value: 2.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 136 NGNPVDDFASKSFPNKGVSIYHL-----AKA-SPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGD 209
Cdd:COG0739   76 KGRITSGFGYRRHPVTGRRRFHKgidiaAPTgTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQ 155

                         90
                 ....*....|..
gi 499427839 210 FVTKGQVIGYSG 221
Cdd:COG0739  156 RVKAGQVIGYVG 167
EnvC super family cl34844
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 35-231 2.59e-14

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


The actual alignment was detected with superfamily member COG4942:

Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 72.10  E-value: 2.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839  35 MISMVILYFVMAHFLMSELEVILANNNQVRENFQSIYEKNSALERDIDYKTNEFLKVNTKVSELESIVNVRKHSNELYNN 114
Cdd:COG4942  134 AVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAA 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 115 Q----DIDIDALTPLQKDMILKIIPNGN----------------PVDDFASKSF--------PNKGVSIYHlAKASPVYA 166
Cdd:COG4942  214 ElaelQQEAEELEALIARLEAEAAAAAErtpaagfaalkgklpwPVSGRVVRRFgerdggggRNKGIDIAA-PPGAPVRA 292

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 167 TANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSGV-----GAGLYYDLR 231
Cdd:COG4942  293 VADGTVVYAGWLRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSsggqgGPTLYFELR 362
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 136-221 2.25e-18

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 81.17  E-value: 2.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 136 NGNPVDDFASKSFPNKGVSIYHL-----AKA-SPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGD 209
Cdd:COG0739   76 KGRITSGFGYRRHPVTGRRRFHKgidiaAPTgTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQ 155

                         90
                 ....*....|..
gi 499427839 210 FVTKGQVIGYSG 221
Cdd:COG0739  156 RVKAGQVIGYVG 167
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 162-221 1.27e-17

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 [Multi-domain]  Cd Length: 85  Bit Score: 75.71  E-value: 1.27e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 162 SPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSG 221
Cdd:cd12797   12 TPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVG 71
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 149-231 2.15e-16

Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.


Pssm-ID: 460250 [Multi-domain]  Cd Length: 96  Bit Score: 72.96  E-value: 2.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839  149 PNKGVSIyHLAKASPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSG-----VG 223
Cdd:pfam01551   2 FHKGIDI-AAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGstgrsTG 80


                  ....*...
gi 499427839  224 AGLYYDLR 231
Cdd:pfam01551  81 PHLHFEIR 88
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 35-231 2.59e-14

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 72.10  E-value: 2.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839  35 MISMVILYFVMAHFLMSELEVILANNNQVRENFQSIYEKNSALERDIDYKTNEFLKVNTKVSELESIVNVRKHSNELYNN 114
Cdd:COG4942  134 AVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAA 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 115 Q----DIDIDALTPLQKDMILKIIPNGN----------------PVDDFASKSF--------PNKGVSIYHlAKASPVYA 166
Cdd:COG4942  214 ElaelQQEAEELEALIARLEAEAAAAAErtpaagfaalkgklpwPVSGRVVRRFgerdggggRNKGIDIAA-PPGAPVRA 292

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 167 TANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSGV-----GAGLYYDLR 231
Cdd:COG4942  293 VADGTVVYAGWLRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSsggqgGPTLYFELR 362
PRK11649 PRK11649
putative peptidase; Provisional
 138-230 1.11e-05

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 46.20  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 138 NPVddfASKSFPNKGVSiYHLAKASPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVI 217
Cdd:PRK11649 304 NPV---TGRVAPHRGVD-FAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKRGDRI 379

                         90
                 ....*....|....*...
gi 499427839 218 GYSG-----VGAGLYYDL 230
Cdd:PRK11649 380 ALSGntgrsTGPHLHYEV 397
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 136-221 2.25e-18

Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440502 [Multi-domain]  Cd Length: 196  Bit Score: 81.17  E-value: 2.25e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 136 NGNPVDDFASKSFPNKGVSIYHL-----AKA-SPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGD 209
Cdd:COG0739   76 KGRITSGFGYRRHPVTGRRRFHKgidiaAPTgTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQ 155

                         90
                 ....*....|..
gi 499427839 210 FVTKGQVIGYSG 221
Cdd:COG0739  156 RVKAGQVIGYVG 167
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 162-221 1.27e-17

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 [Multi-domain]  Cd Length: 85  Bit Score: 75.71  E-value: 1.27e-17
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 162 SPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSG 221
Cdd:cd12797   12 TPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVG 71
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 149-231 2.15e-16

Peptidase family M23; Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins such as Swiss:P33648 for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.


Pssm-ID: 460250 [Multi-domain]  Cd Length: 96  Bit Score: 72.96  E-value: 2.15e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839  149 PNKGVSIyHLAKASPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSG-----VG 223
Cdd:pfam01551   2 FHKGIDI-AAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGstgrsTG 80


                  ....*...
gi 499427839  224 AGLYYDLR 231
Cdd:pfam01551  81 PHLHFEIR 88
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 35-231 2.59e-14

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 72.10  E-value: 2.59e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839  35 MISMVILYFVMAHFLMSELEVILANNNQVRENFQSIYEKNSALERDIDYKTNEFLKVNTKVSELESIVNVRKHSNELYNN 114
Cdd:COG4942  134 AVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAA 213

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 115 Q----DIDIDALTPLQKDMILKIIPNGN----------------PVDDFASKSF--------PNKGVSIYHlAKASPVYA 166
Cdd:COG4942  214 ElaelQQEAEELEALIARLEAEAAAAAErtpaagfaalkgklpwPVSGRVVRRFgerdggggRNKGIDIAA-PPGAPVRA 292

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 167 TANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVIGYSGV-----GAGLYYDLR 231
Cdd:COG4942  293 VADGTVVYAGWLRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSsggqgGPTLYFELR 362
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 150-223 2.65e-08

Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444523 [Multi-domain]  Cd Length: 200  Bit Score: 53.11  E-value: 2.65e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 499427839 150 NKGVSIyHLAKASPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLR-KVIVQKGDFVTKGQVIGysGVG 223
Cdd:COG5821   97 HTGIDI-AAKEGTPVKAAADGVVVEVGKDPKYGITVVIDHGNGIKTVYANLDsKIKVKVGQKVKKGQVIG--KVG 168
SpoIVFA COG5833
Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, ...
 136-234 4.76e-06

Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444535 [Multi-domain]  Cd Length: 219  Bit Score: 46.52  E-value: 4.76e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 136 NGNPVDDFASKsfpNKGVSIyHLAKASPVYATANGIidsVRVAGSENQF---VQIQHSYGFTSNYGHLRKVIVQKGDFVT 212
Cdd:COG5833  109 SGKVVESFQEN---GKGVDI-ETPGGANVKAVKEGY---VIFAGKDEETgktVIIQHADGSESWYGNLSSIDVKLYDFVE 181

                         90       100       110
                 ....*....|....*....|....*....|
gi 499427839 213 KGQVIGYSGVGA---GLYY-----DLRFID 234
Cdd:COG5833  182 AGQKIGTVPATEgeeGTFYfaikkGGKFID 211
PRK11649 PRK11649
putative peptidase; Provisional
 138-230 1.11e-05

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 46.20  E-value: 1.11e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499427839 138 NPVddfASKSFPNKGVSiYHLAKASPVYATANGIIDSVRVAGSENQFVQIQHSYGFTSNYGHLRKVIVQKGDFVTKGQVI 217
Cdd:PRK11649 304 NPV---TGRVAPHRGVD-FAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKRGDRI 379

                         90
                 ....*....|....*...
gi 499427839 218 GYSG-----VGAGLYYDL 230
Cdd:PRK11649 380 ALSGntgrsTGPHLHYEV 397
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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