NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|499503183|ref|WP_011189823|]
View 

M23 family metallopeptidase [Desulfotalea psychrophila]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
 324-442 1.85e-37

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: 135.49  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 324 AGFAERRSYYYKNRlidkQVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGED 403
Cdd:COG0739   81 SGFGYRRHPVTGRR----RFHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQR 156

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499503183 404 VTKGATIGLTGATGMAGGDHLHFSILVHGTFVNPREWWD 442
Cdd:COG0739  157 VKAGQVIGYVGNTGRSTGPHLHFEVRVNGKPVDPLPFLP 195
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 324-442 1.85e-37

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: 135.49  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 324 AGFAERRSYYYKNRlidkQVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGED 403
Cdd:COG0739   81 SGFGYRRHPVTGRR----RFHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQR 156

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499503183 404 VTKGATIGLTGATGMAGGDHLHFSILVHGTFVNPREWWD 442
Cdd:COG0739  157 VKAGQVIGYVGNTGRSTGPHLHFEVRVNGKPVDPLPFLP 195
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 342-437 6.35e-32

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: 117.26  E-value: 6.35e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183  342 QVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGG 421
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRSTG 80

                          90
                  ....*....|....*.
gi 499503183  422 DHLHFSILVHGTFVNP 437
Cdd:pfam01551  81 PHLHFEIRKNGKPVDP 96
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 344-428 1.39e-28

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: 107.68  E-value: 1.39e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 344 HLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDH 423
Cdd:cd12797    1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTGPH 80


                 ....*
gi 499503183 424 LHFSI 428
Cdd:cd12797   81 LHFEI 85
PRK11637 PRK11637
AmiB activator; Provisional
 346-443 7.72e-12

AmiB activator; Provisional


Pssm-ID: 236942 [Multi-domain]  Cd Length: 428  Bit Score: 67.03  E-value: 7.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 346 GMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDHLH 425
Cdd:PRK11637 331 GMVIGASEGTEVKAIADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGAQVRAGQPIALVGSSGGQGRPSLY 410

                         90
                 ....*....|....*...
gi 499503183 426 FSILVHGTFVNPREWWDR 443
Cdd:PRK11637 411 FEIRRQGQAVNPQPWLGR 428
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 324-442 1.85e-37

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: 135.49  E-value: 1.85e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 324 AGFAERRSYYYKNRlidkQVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGED 403
Cdd:COG0739   81 SGFGYRRHPVTGRR----RFHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSSILVKVGQR 156

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 499503183 404 VTKGATIGLTGATGMAGGDHLHFSILVHGTFVNPREWWD 442
Cdd:COG0739  157 VKAGQVIGYVGNTGRSTGPHLHFEVRVNGKPVDPLPFLP 195
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 295-444 1.12e-33

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: 130.27  E-value: 1.12e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 295 NAAIAKIC--ETSEPNRLWQGRFGRMAGSSP--------AGFAERRSYYYKNRlidkqvhlGMDLASTRRAHVKASNTGK 364
Cdd:COG4942  226 EALIARLEaeAAAAAERTPAAGFAALKGKLPwpvsgrvvRRFGERDGGGGRNK--------GIDIAAPPGAPVRAVADGT 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 365 VVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDHLHFSILVHGTFVNPREWWDRK 444
Cdd:COG4942  298 VVYAGWLRGYGNLVIIDHGGGYLTLYAHLSSLLVKVGQRVKAGQPIGTVGSSGGQGGPTLYFELRKNGKPVDPLPWLAKR 377
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 342-437 6.35e-32

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: 117.26  E-value: 6.35e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183  342 QVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGG 421
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRSTG 80

                          90
                  ....*....|....*.
gi 499503183  422 DHLHFSILVHGTFVNP 437
Cdd:pfam01551  81 PHLHFEIRKNGKPVDP 96
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 344-428 1.39e-28

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: 107.68  E-value: 1.39e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 344 HLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDH 423
Cdd:cd12797    1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTGPH 80


                 ....*
gi 499503183 424 LHFSI 428
Cdd:cd12797   81 LHFEI 85
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 325-437 1.25e-21

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: 92.40  E-value: 1.25e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 325 GFAERRSYYykNRLIDKQVHLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHL-SQINVAVGED 403
Cdd:COG5821   80 EFGEDLVYS--KTLNEWRTHTGIDIAAKEGTPVKAAADGVVVEVGKDPKYGITVVIDHGNGIKTVYANLdSKIKVKVGQK 157

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 499503183 404 VTKGATIGLTGATG---MAGGDHLHFSILVHGTFVNP 437
Cdd:COG5821  158 VKKGQVIGKVGSTAlfeSSEGPHLHFEVLKNGKPVDP 194
SpoIIQ COG5820
Stage II sporulation protein SpoIIQ, required for engulfement [Cell cycle control, cell ...
 344-442 2.44e-12

Stage II sporulation protein SpoIIQ, required for engulfement [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444522 [Multi-domain]  Cd Length: 224  Bit Score: 66.10  E-value: 2.44e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 344 HLGMDLASTRRA--HVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGAT--GMA 419
Cdd:COG5820  120 STGIDIAAKDGEsfDVLAALSGTVTEVEEDPLLGYVVEIKHDNGVSTVYQSLSDVKVKAGDEVKQGQVIGTAGRNlfNKD 199

                         90       100
                 ....*....|....*....|...
gi 499503183 420 GGDHLHFSILVHGTFVNPREWWD 442
Cdd:COG5820  200 AGVHLHFEVRKDGKAVNPESYLP 222
PRK11637 PRK11637
AmiB activator; Provisional
 346-443 7.72e-12

AmiB activator; Provisional


Pssm-ID: 236942 [Multi-domain]  Cd Length: 428  Bit Score: 67.03  E-value: 7.72e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 346 GMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDHLH 425
Cdd:PRK11637 331 GMVIGASEGTEVKAIADGRVLLADWLQGYGLVVVVEHGKGDMSLYGYNQSALVSVGAQVRAGQPIALVGSSGGQGRPSLY 410

                         90
                 ....*....|....*...
gi 499503183 426 FSILVHGTFVNPREWWDR 443
Cdd:PRK11637 411 FEIRRQGQAVNPQPWLGR 428
PRK11649 PRK11649
putative peptidase; Provisional
 344-437 5.96e-11

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 64.30  E-value: 5.96e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 344 HLGMDLASTRRAHVKASNTGKVVHADYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAGGDH 423
Cdd:PRK11649 313 HRGVDFAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTTRYMHLRKLLVKPGQKVKRGDRIALSGNTGRSTGPH 392

                         90
                 ....*....|....
gi 499503183 424 LHFSILVHGTFVNP 437
Cdd:PRK11649 393 LHYEVWINQQAVNP 406
nlpD PRK10871
murein hydrolase activator NlpD;
346-437 4.94e-08

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 54.46  E-value: 4.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499503183 346 GMDLASTRRAHVKASNTGKVVHA-DYLGIYGNMIMLDHGQGIFSLYSHLSQINVAVGEDVTKGATIGLTGATGMAgGDHL 424
Cdd:PRK10871 221 GIDIAGSKGQAIIATADGRVVYAgNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTS-STRL 299

                         90
                 ....*....|...
gi 499503183 425 HFSILVHGTFVNP 437
Cdd:PRK10871 300 HFEIRYKGKSVNP 312
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH