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Conserved domains on  [gi|499769629|ref|WP_011450363|]
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M23 family metallopeptidase [Anaplasma phagocytophilum]

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 ...
 88-216 1.40e-21

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: 88.11  E-value: 1.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  88 MPLNGKVVS---MQSFGNTGGVRCESGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYNLDEIGV 164
Cdd:COG0739   73 WPVKGRITSgfgYRRHPVTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWN-GGYGNLVIIDHGNGYTTLYAHLSSILV 151

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499769629 165 KIGDSVNKGDVLATIASS-YAGGkalsegntPFCCFSMRHDGKEVDTVQHLKQ 216
Cdd:COG0739  152 KVGQRVKAGQVIGYVGNTgRSTG--------PHLHFEVRVNGKPVDPLPFLPA 196
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 88-216 1.40e-21

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: 88.11  E-value: 1.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  88 MPLNGKVVS---MQSFGNTGGVRCESGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYNLDEIGV 164
Cdd:COG0739   73 WPVKGRITSgfgYRRHPVTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWN-GGYGNLVIIDHGNGYTTLYAHLSSILV 151

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499769629 165 KIGDSVNKGDVLATIASS-YAGGkalsegntPFCCFSMRHDGKEVDTVQHLKQ 216
Cdd:COG0739  152 KVGQRVKAGQVIGYVGNTgRSTG--------PHLHFEVRVNGKPVDPLPFLPA 196
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 110-182 2.37e-16

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: 71.08  E-value: 2.37e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499769629 110 SGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASS 182
Cdd:cd12797    2 NGIDIAAPEGTPVYAAADGTVVFAGWD-GGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNT 73
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 122-209 2.84e-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: 71.42  E-value: 2.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  122 VTASSRGKVMYVGkNLRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASS-YAGGKALsegntpfcCFS 200
Cdd:pfam01551  16 VYAAADGVVVFAG-WLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTgRSTGPHL--------HFE 86


                  ....*....
gi 499769629  201 MRHDGKEVD 209
Cdd:pfam01551  87 IRKNGKPVD 95
nlpD PRK10871
murein hydrolase activator NlpD;
49-216 1.91e-09

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 56.38  E-value: 1.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  49 NSTPTGRSTAKPglvlVEDASTSNMDPVVYEARPGCDFSM---PLNGKVVsmQSFGNT-GGvrcESGVAII-SKGDiEVT 123
Cdd:PRK10871 164 NNKPAATTVTAP----VTAPTASTTEPTASSTSTSTPISTwrwPTDGKVI--ENFSASeGG---NKGIDIAgSKGQ-AII 233

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629 124 ASSRGKVMYVGKNLRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASSYAGGKALSegntpfccFSMRH 203
Cdd:PRK10871 234 ATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLH--------FEIRY 305

                        170
                 ....*....|...
gi 499769629 204 DGKEVDTVQHLKQ 216
Cdd:PRK10871 306 KGKSVNPLRYLPQ 318
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 88-216 1.40e-21

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: 88.11  E-value: 1.40e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  88 MPLNGKVVS---MQSFGNTGGVRCESGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYNLDEIGV 164
Cdd:COG0739   73 WPVKGRITSgfgYRRHPVTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWN-GGYGNLVIIDHGNGYTTLYAHLSSILV 151

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 499769629 165 KIGDSVNKGDVLATIASS-YAGGkalsegntPFCCFSMRHDGKEVDTVQHLKQ 216
Cdd:COG0739  152 KVGQRVKAGQVIGYVGNTgRSTG--------PHLHFEVRVNGKPVDPLPFLPA 196
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 86-209 6.70e-21

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: 89.44  E-value: 6.70e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  86 FSMPLNGKVVSmqSFGN-TGGVRCESGVAIISKGDIEVTASSRGKVMYVGkNLRKYGNLVILEHDRYTITMYYNLDEIGV 164
Cdd:COG4942  255 LPWPVSGRVVR--RFGErDGGGGRNKGIDIAAPPGAPVRAVADGTVVYAG-WLRGYGNLVIIDHGGGYLTLYAHLSSLLV 331

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 499769629 165 KIGDSVNKGDVLATIASSyaggkalSEGNTPFCCFSMRHDGKEVD 209
Cdd:COG4942  332 KVGQRVKAGQPIGTVGSS-------GGQGGPTLYFELRKNGKPVD 369
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 86-216 1.16e-17

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: 77.76  E-value: 1.16e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  86 FSMPLNGKVVSmqSFGN-------TGGVRCESGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYN 158
Cdd:COG5821   69 FLKPVSGKITR--EFGEdlvysktLNEWRTHTGIDIAAKEGTPVKAAADGVVVEVGKD-PKYGITVVIDHGNGIKTVYAN 145

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 499769629 159 LD-EIGVKIGDSVNKGDVLATIASSyaGGKALSEGntPFCCFSMRHDGKEVDTVQHLKQ 216
Cdd:COG5821  146 LDsKIKVKVGQKVKKGQVIGKVGST--ALFESSEG--PHLHFEVLKNGKPVDPMKYLKK 200
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 110-182 2.37e-16

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: 71.08  E-value: 2.37e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499769629 110 SGVAIISKGDIEVTASSRGKVMYVGKNlRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASS 182
Cdd:cd12797    2 NGIDIAAPEGTPVYAAADGTVVFAGWD-GGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNT 73
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 122-209 2.84e-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: 71.42  E-value: 2.84e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  122 VTASSRGKVMYVGkNLRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASS-YAGGKALsegntpfcCFS 200
Cdd:pfam01551  16 VYAAADGVVVFAG-WLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTgRSTGPHL--------HFE 86


                  ....*....
gi 499769629  201 MRHDGKEVD 209
Cdd:pfam01551  87 IRKNGKPVD 95
nlpD PRK10871
murein hydrolase activator NlpD;
49-216 1.91e-09

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 56.38  E-value: 1.91e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  49 NSTPTGRSTAKPglvlVEDASTSNMDPVVYEARPGCDFSM---PLNGKVVsmQSFGNT-GGvrcESGVAII-SKGDiEVT 123
Cdd:PRK10871 164 NNKPAATTVTAP----VTAPTASTTEPTASSTSTSTPISTwrwPTDGKVI--ENFSASeGG---NKGIDIAgSKGQ-AII 233

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629 124 ASSRGKVMYVGKNLRKYGNLVILEHDRYTITMYYNLDEIGVKIGDSVNKGDVLATIASSYAGGKALSegntpfccFSMRH 203
Cdd:PRK10871 234 ATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVREQQEVKAGQKIATMGSTGTSSTRLH--------FEIRY 305

                        170
                 ....*....|...
gi 499769629 204 DGKEVDTVQHLKQ 216
Cdd:PRK10871 306 KGKSVNPLRYLPQ 318
PRK11649 PRK11649
putative peptidase; Provisional
 83-177 2.02e-03

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 38.49  E-value: 2.02e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  83 GCDFSMPLngkvvsmqsfgntggvrcesGVAIISKGDIEVTASSRGKVMyvgknlrkyGNLVILEHDRYTITMYYNLDEI 162
Cdd:PRK11649 315 GVDFAMPV--------------------GTPVLAVGDGEVVVAKRSGAA---------GNYVAIRHGRQYTTRYMHLRKL 365

                         90
                 ....*....|....*
gi 499769629 163 GVKIGDSVNKGDVLA 177
Cdd:PRK11649 366 LVKPGQKVKRGDRIA 380
rpoB PRK00405
DNA-directed RNA polymerase subunit beta; Reviewed
 110-177 3.12e-03

DNA-directed RNA polymerase subunit beta; Reviewed


Pssm-ID: 234749 [Multi-domain]  Cd Length: 1112  Bit Score: 38.16  E-value: 3.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499769629  110 SGVAIISKGDievtassrGKVMYV-GKNLR-KYGNLVILE--HDRYTITMY--------YNLDEIgVKIGDSVNKGDVLA 177
Cdd:PRK00405  633 SGAVVVAKRD--------GVVEYVdASRIVvRVEELDPGEdgVDIYNLIKFqrsnqntcINQRPI-VKVGDRVEKGDVLA 703
 
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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