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Conserved domains on  [gi|1141960711|gb|AQD19567|]
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peptidase M23 [Staphylococcus aureus]

Protein Classification

M23 family metallopeptidase( domain architecture ID 11432770)

M23 family metallopeptidase lyses bacterial cell wall peptidoglycans

EC:  3.4.24.-
Gene Ontology:  GO:0046872|GO:0008237
MEROPS:  M23
PubMed:  36386627

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 ...
 58-181 5.63e-39

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: 132.02  E-value: 5.63e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  58 SRITETFGkYQHSPFDGK---HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHqWYLHLDKYNVKVG 134
Cdd:COG0739    77 GRITSGFG-YRRHPVTGRrrfHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTT-LYAHLSSILVKVG 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1141960711 135 DRVKAGDIIAYSGNTGkQTTGAHLHFQRMKGGVgnayAEDPKPFIDQ 181
Cdd:COG0739   155 QRVKAGQVIGYVGNTG-RSTGPHLHFEVRVNGK----PVDPLPFLPA 196
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 58-181 5.63e-39

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: 132.02  E-value: 5.63e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  58 SRITETFGkYQHSPFDGK---HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHqWYLHLDKYNVKVG 134
Cdd:COG0739    77 GRITSGFG-YRRHPVTGRrrfHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTT-LYAHLSSILVKVG 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1141960711 135 DRVKAGDIIAYSGNTGkQTTGAHLHFQRMKGGVgnayAEDPKPFIDQ 181
Cdd:COG0739   155 QRVKAGQVIGYVGNTG-RSTGPHLHFEVRVNGK----PVDPLPFLPA 196
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 74-167 5.67e-34

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: 116.11  E-value: 5.67e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  74 GKHYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGeYHQWYLHLDKYNVKVGDRVKAGDIIAYSGNTGkQT 153
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNG-YSTLYAHLSSILVKVGQRVKAGQVIGTVGSTG-RS 78

                          90
                  ....*....|....
gi 1141960711 154 TGAHLHFQRMKGGV 167
Cdd:pfam01551  79 TGPHLHFEIRKNGK 92
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 76-161 6.11e-33

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: 113.07  E-value: 6.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  76 HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGeYHQWYLHLDKYNVKVGDRVKAGDIIAYSGNTGkQTTG 155
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNG-YYTLYAHLSSILVKVGQRVKKGQVIGTVGNTG-RSTG 78


                  ....*.
gi 1141960711 156 AHLHFQ 161
Cdd:cd12797    79 PHLHFE 84
PRK11649 PRK11649
putative peptidase; Provisional
 59-161 5.23e-18

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 80.86  E-value: 5.23e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  59 RITETFGKYQHSPFDGK---HYGVDFALPKGTPIKAPTNGKVtrIFNNELGGKVLQIAEDNG-EYHQWYLHLDKYNVKVG 134
Cdd:PRK11649  293 RISSNFNPRRLNPVTGRvapHRGVDFAMPVGTPVLAVGDGEV--VVAKRSGAAGNYVAIRHGrQYTTRYMHLRKLLVKPG 370

                          90       100
                  ....*....|....*....|....*..
gi 1141960711 135 DRVKAGDIIAYSGNTGKqTTGAHLHFQ 161
Cdd:PRK11649  371 QKVKRGDRIALSGNTGR-STGPHLHYE 396
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 58-181 5.63e-39

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: 132.02  E-value: 5.63e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  58 SRITETFGkYQHSPFDGK---HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHqWYLHLDKYNVKVG 134
Cdd:COG0739    77 GRITSGFG-YRRHPVTGRrrfHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTT-LYAHLSSILVKVG 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1141960711 135 DRVKAGDIIAYSGNTGkQTTGAHLHFQRMKGGVgnayAEDPKPFIDQ 181
Cdd:COG0739   155 QRVKAGQVIGYVGNTG-RSTGPHLHFEVRVNGK----PVDPLPFLPA 196
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 74-167 5.67e-34

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: 116.11  E-value: 5.67e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  74 GKHYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGeYHQWYLHLDKYNVKVGDRVKAGDIIAYSGNTGkQT 153
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNG-YSTLYAHLSSILVKVGQRVKAGQVIGTVGSTG-RS 78

                          90
                  ....*....|....
gi 1141960711 154 TGAHLHFQRMKGGV 167
Cdd:pfam01551  79 TGPHLHFEIRKNGK 92
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 76-161 6.11e-33

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: 113.07  E-value: 6.11e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  76 HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGeYHQWYLHLDKYNVKVGDRVKAGDIIAYSGNTGkQTTG 155
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNG-YYTLYAHLSSILVKVGQRVKKGQVIGTVGNTG-RSTG 78


                  ....*.
gi 1141960711 156 AHLHFQ 161
Cdd:cd12797    79 PHLHFE 84
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 59-179 7.82e-25

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: 99.07  E-value: 7.82e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  59 RITETFGKYQhsPFDGKHYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIaEDNGEYHQWYLHLDKYNVKVGDRVK 138
Cdd:COG4942   262 RVVRRFGERD--GGGGRNKGIDIAAPPGAPVRAVADGTVVYAGWLRGYGNLVII-DHGGGYLTLYAHLSSLLVKVGQRVK 338

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1141960711 139 AGDIIAYSGNTGKQtTGAHLHFQRMKGGVgnayAEDPKPFI 179
Cdd:COG4942   339 AGQPIGTVGSSGGQ-GGPTLYFELRKNGK----PVDPLPWL 374
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 59-179 1.31e-24

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: 95.09  E-value: 1.31e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  59 RITETFGKY-QHSPFDGK---HYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGeYHQWYLHLD-KYNVKV 133
Cdd:COG5821    76 KITREFGEDlVYSKTLNEwrtHTGIDIAAKEGTPVKAAADGVVVEVGKDPKYGITVVIDHGNG-IKTVYANLDsKIKVKV 154

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1141960711 134 GDRVKAGDIIAYSGNTGK--QTTGAHLHFQRMKGGVgnayAEDPKPFI 179
Cdd:COG5821   155 GQKVKKGQVIGKVGSTALfeSSEGPHLHFEVLKNGK----PVDPMKYL 198
PRK11649 PRK11649
putative peptidase; Provisional
 59-161 5.23e-18

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 80.86  E-value: 5.23e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  59 RITETFGKYQHSPFDGK---HYGVDFALPKGTPIKAPTNGKVtrIFNNELGGKVLQIAEDNG-EYHQWYLHLDKYNVKVG 134
Cdd:PRK11649  293 RISSNFNPRRLNPVTGRvapHRGVDFAMPVGTPVLAVGDGEV--VVAKRSGAAGNYVAIRHGrQYTTRYMHLRKLLVKPG 370

                          90       100
                  ....*....|....*....|....*..
gi 1141960711 135 DRVKAGDIIAYSGNTGKqTTGAHLHFQ 161
Cdd:PRK11649  371 QKVKRGDRIALSGNTGR-STGPHLHYE 396
nlpD PRK10871
murein hydrolase activator NlpD;
59-165 2.58e-08

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 52.53  E-value: 2.58e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711  59 RITETFGKYQhspfdGKHYGVDFALPKGTPIKAPTNGKVTRIFNNELGGKVLQIAEDNGEYHQWYLHLDKYNVKVGDRVK 138
Cdd:PRK10871  207 KVIENFSASE-----GGNKGIDIAGSKGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVK 281

                          90       100
                  ....*....|....*....|....*...
gi 1141960711 139 AGDIIAYSGNTGkqTTGAHLHFQ-RMKG 165
Cdd:PRK10871  282 AGQKIATMGSTG--TSSTRLHFEiRYKG 307
PRK06148 PRK06148
hypothetical protein; Provisional
 76-161 2.27e-06

hypothetical protein; Provisional


Pssm-ID: 180426 [Multi-domain]  Cd Length: 1013  Bit Score: 46.94  E-value: 2.27e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1141960711   76 HYGVDFALPKGTPIKAPTNGKVTRIFNNEL----GGKV-LQIAEDNGE-YHQWYLHLDKYNV---KVGDRVKAGDIIAYS 146
Cdd:PRK06148   441 HLGVDLFAPAGTPVYAPLAGTVRSVEIEAVplgyGGLVaLEHETPGGDpFYTLYGHLAHEAVsrlKPGDRLAAGELFGAM 520

                           90
                   ....*....|....*....
gi 1141960711  147 G----NTGKQttgAHLHFQ 161
Cdd:PRK06148   521 GdaheNGGWA---PHLHFQ 536
 
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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