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Conserved domains on  [gi|255929150|ref|YP_003097462|]
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2OG-Fe(II) oxygenase family like protein [Synechococcus phage S-RSM4]

Protein Classification

M23 family metallopeptidase( domain architecture ID 11432770)

M23 family metallopeptidase is an endopeptidase that lyses bacterial cell wall peptidoglycans

EC:  3.4.24.-
Gene Ontology:  GO:0004222
MEROPS:  M23

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 ...
 639-755 3.26e-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: 83.87  E-value: 3.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  639 QHYGASRD---GGDRTHGGIDItdAYSMGDnkaaPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLE 715
Cdd:COG0739    81 SGFGYRRHpvtGRRRFHKGIDI--AAPTGT----PVYAAADGTVVFAGWNGGY-GNLVIIDHGNGYTTLYAHLS-SILVK 152

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 255929150  716 VGQMVHGGQKIAdlhryY---SGGVEQTHLHFQVRENGTIVDP 755
Cdd:COG0739   153 VGQRVKAGQVIG-----YvgnTGRSTGPHLHFEVRVNGKPVDP 190
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 639-755 3.26e-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: 83.87  E-value: 3.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  639 QHYGASRD---GGDRTHGGIDItdAYSMGDnkaaPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLE 715
Cdd:COG0739    81 SGFGYRRHpvtGRRRFHKGIDI--AAPTGT----PVYAAADGTVVFAGWNGGY-GNLVIIDHGNGYTTLYAHLS-SILVK 152

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 255929150  716 VGQMVHGGQKIAdlhryY---SGGVEQTHLHFQVRENGTIVDP 755
Cdd:COG0739   153 VGQRVKAGQVIG-----YvgnTGRSTGPHLHFEVRVNGKPVDP 190
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 650-755 1.40e-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: 76.05  E-value: 1.40e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150   650 RTHGGIDItdAYSMGdnkaAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQMVHGGQKIAdl 729
Cdd:pfam01551    1 RFHKGIDI--AAPTG----TPVYAAADGVVVFAGWLGGY-GNLVIIDHGNGYSTLYAHLS-SILVKVGQRVKAGQVIG-- 70

                           90       100
                   ....*....|....*....|....*....
gi 255929150   730 hryYSG---GVEQTHLHFQVRENGTIVDP 755
Cdd:pfam01551   71 ---TVGstgRSTGPHLHFEIRKNGKPVDP 96
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 652-746 6.43e-14

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: 68.00  E-value: 6.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  652 HGGIDItdAYSMGdnkaAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQMVHGGQKIAdlHR 731
Cdd:cd12797     1 HNGIDI--AAPEG----TPVYAAADGTVVFAGWDGGY-GNYVIIDHGNGYYTLYAHLS-SILVKVGQRVKKGQVIG--TV 70

                          90
                  ....*....|....*
gi 255929150  732 YYSGGVEQTHLHFQV 746
Cdd:cd12797    71 GNTGRSTGPHLHFEI 85
nlpD PRK10871
murein hydrolase activator NlpD;
643-755 6.01e-04

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 43.29  E-value: 6.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  643 ASRDGGDRthgGIDITDAysmgdnKAAPVIAYKSGKITQISTTGGGPGGIVKIDHGNGFATEYFHVDPRSDLEvGQMVHG 722
Cdd:PRK10871  213 SASEGGNK---GIDIAGS------KGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVRE-QQEVKA 282

                          90       100       110
                  ....*....|....*....|....*....|...
gi 255929150  723 GQKIADLHryySGGVEQTHLHFQVRENGTIVDP 755
Cdd:PRK10871  283 GQKIATMG---STGTSSTRLHFEIRYKGKSVNP 312
 
Name Accession Description Interval E-value
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 639-755 3.26e-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: 83.87  E-value: 3.26e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  639 QHYGASRD---GGDRTHGGIDItdAYSMGDnkaaPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLE 715
Cdd:COG0739    81 SGFGYRRHpvtGRRRFHKGIDI--AAPTGT----PVYAAADGTVVFAGWNGGY-GNLVIIDHGNGYTTLYAHLS-SILVK 152

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 255929150  716 VGQMVHGGQKIAdlhryY---SGGVEQTHLHFQVRENGTIVDP 755
Cdd:COG0739   153 VGQRVKAGQVIG-----YvgnTGRSTGPHLHFEVRVNGKPVDP 190
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 650-756 9.06e-18

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: 82.77  E-value: 9.06e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  650 RTHGGIDItdAYSMGdnkaAPVIAYKSGKITQISTtGGGPGGIVKIDHGNGFATEYFHVDPRSDLEVGQMVHGGQKIadl 729
Cdd:COG5821    95 RTHTGIDI--AAKEG----TPVKAAADGVVVEVGK-DPKYGITVVIDHGNGIKTVYANLDSKIKVKVGQKVKKGQVI--- 164

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 255929150  730 hryysGGV---------EQTHLHFQVRENGTIVDPT 756
Cdd:COG5821   165 -----GKVgstalfessEGPHLHFEVLKNGKPVDPM 195
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 650-755 1.40e-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: 76.05  E-value: 1.40e-16
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150   650 RTHGGIDItdAYSMGdnkaAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQMVHGGQKIAdl 729
Cdd:pfam01551    1 RFHKGIDI--AAPTG----TPVYAAADGVVVFAGWLGGY-GNLVIIDHGNGYSTLYAHLS-SILVKVGQRVKAGQVIG-- 70

                           90       100
                   ....*....|....*....|....*....
gi 255929150   730 hryYSG---GVEQTHLHFQVRENGTIVDP 755
Cdd:pfam01551   71 ---TVGstgRSTGPHLHFEIRKNGKPVDP 96
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 652-746 6.43e-14

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: 68.00  E-value: 6.43e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  652 HGGIDItdAYSMGdnkaAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQMVHGGQKIAdlHR 731
Cdd:cd12797     1 HNGIDI--AAPEG----TPVYAAADGTVVFAGWDGGY-GNYVIIDHGNGYYTLYAHLS-SILVKVGQRVKKGQVIG--TV 70

                          90
                  ....*....|....*
gi 255929150  732 YYSGGVEQTHLHFQV 746
Cdd:cd12797    71 GNTGRSTGPHLHFEI 85
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 639-755 1.57e-13

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: 73.64  E-value: 1.57e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  639 QHYGASRDGGdRTHGGIDItdaysmGDNKAAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQ 718
Cdd:COG4942   265 RRFGERDGGG-GRNKGIDI------AAPPGAPVRAVADGTVVYAGWLRGY-GNLVIIDHGGGYLTLYAHLS-SLLVKVGQ 335

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 255929150  719 MVHGGQKIADLHRyySGGVEQTHLHFQVRENGTIVDP 755
Cdd:COG4942   336 RVKAGQPIGTVGS--SGGQGGPTLYFELRKNGKPVDP 370
nlpD PRK10871
murein hydrolase activator NlpD;
643-755 6.01e-04

murein hydrolase activator NlpD;


Pssm-ID: 236782 [Multi-domain]  Cd Length: 319  Bit Score: 43.29  E-value: 6.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  643 ASRDGGDRthgGIDITDAysmgdnKAAPVIAYKSGKITQISTTGGGPGGIVKIDHGNGFATEYFHVDPRSDLEvGQMVHG 722
Cdd:PRK10871  213 SASEGGNK---GIDIAGS------KGQAIIATADGRVVYAGNALRGYGNLIIIKHNDDYLSAYAHNDTMLVRE-QQEVKA 282

                          90       100       110
                  ....*....|....*....|....*....|...
gi 255929150  723 GQKIADLHryySGGVEQTHLHFQVRENGTIVDP 755
Cdd:PRK10871  283 GQKIATMG---STGTSSTRLHFEIRYKGKSVNP 312
SpoIVFA COG5833
Stage IV sporulation protein SpoIVFA, regulates SpoIVFB [Cell cycle control, cell division, ...
 651-756 3.55e-03

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


Pssm-ID: 444535 [Multi-domain]  Cd Length: 219  Bit Score: 39.97  E-value: 3.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 255929150  651 THGGIDITDaysmgdNKAAPVIAYKSGKITQISTTGGGpGGIVKIDHGNGFATEYFHVDpRSDLEVGQMVHGGQKIadlh 730
Cdd:COG5833   119 NGKGVDIET------PGGANVKAVKEGYVIFAGKDEET-GKTVIIQHADGSESWYGNLS-SIDVKLYDFVEAGQKI---- 186

                          90       100       110
                  ....*....|....*....|....*....|.
gi 255929150  731 ryysGGVEQT-----HLHFQVRENGTIVDPT 756
Cdd:COG5833   187 ----GTVPATegeegTFYFAIKKGGKFIDPI 213
 
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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