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Conserved domains on  [gi|2126616135|gb|UDV65555|]
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peptidoglycan DD-metalloendopeptidase family protein (plasmid) [Enterobacter hormaechei]

Protein Classification

peptidoglycan DD-metalloendopeptidase family protein( domain architecture ID 1003011)

peptidoglycan DD-metalloendopeptidase family protein similar to Vibrio cholerae LysM/M23 family peptidase ShyA

CATH:  3.10.450.350|2.70.70.10
EC:  3.4.24.-
Gene Ontology:  GO:0004222|GO:0046872|GO:0042834|GO:0006508
MEROPS:  M23
SCOP:  4004548|4000931

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
PRK11649 super family cl36042
putative peptidase; Provisional
 14-217 9.25e-62

putative peptidase; Provisional


The actual alignment was detected with superfamily member PRK11649:

Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 199.89  E-value: 9.25e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  14 SATRSGLESNEIATLQRSLPSRFNLRHLKKNESLKL-----VLQKKAGKSRVVAYKFTSGSFNYTAYRISDKKFYNLSDT 88
Cdd:PRK11649  198 SAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVlmsreMLDGKSEQSQLLGVRLRSGGKDYYAIRAEDGKFYDRNGS 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  89 S-GKGSLDYPLPATARLSSPFNPARLNPVSGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKT 167
Cdd:PRK11649  278 GlAKGFLRFPTAKQFRISSNFNPRRLNPVTGRVAPHRGVDFAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTT 357

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2126616135 168 RYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSL 217
Cdd:PRK11649  358 RYMHLRKLLVKPGQKVKRGDRIALSGNTGRSTGPHLHYEVWINQQAVNPL 407
 
Name Accession Description Interval E-value
PRK11649 PRK11649
putative peptidase; Provisional
 14-217 9.25e-62

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 199.89  E-value: 9.25e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  14 SATRSGLESNEIATLQRSLPSRFNLRHLKKNESLKL-----VLQKKAGKSRVVAYKFTSGSFNYTAYRISDKKFYNLSDT 88
Cdd:PRK11649  198 SAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVlmsreMLDGKSEQSQLLGVRLRSGGKDYYAIRAEDGKFYDRNGS 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  89 S-GKGSLDYPLPATARLSSPFNPARLNPVSGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKT 167
Cdd:PRK11649  278 GlAKGFLRFPTAKQFRISSNFNPRRLNPVTGRVAPHRGVDFAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTT 357

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2126616135 168 RYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSL 217
Cdd:PRK11649  358 RYMHLRKLLVKPGQKVKRGDRIALSGNTGRSTGPHLHYEVWINQQAVNPL 407
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 95-219 1.79e-46

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: 153.20  E-value: 1.79e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  95 DYPLPATARLSSPFNPaRLNPVSGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNK 174
Cdd:COG0739    70 SGAWPVKGRITSGFGY-RRHPVTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSS 148

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2126616135 175 ILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSLAF 219
Cdd:COG0739   149 ILVKVGQRVKAGQVIGYVGNTGRSTGPHLHFEVRVNGKPVDPLPF 193
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 121-215 4.16e-35

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: 120.73  E-value: 4.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 121 SPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSG 200
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRSTG 80

                          90
                  ....*....|....*
gi 2126616135 201 PHLHYELVINNNPVN 215
Cdd:pfam01551  81 PHLHFEIRKNGKPVD 95
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 123-207 2.70e-34

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: 118.08  E-value: 2.70e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 123 HNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPH 202
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTGPH 80


                  ....*
gi 2126616135 203 LHYEL 207
Cdd:cd12797    81 LHFEI 85
 
Name Accession Description Interval E-value
PRK11649 PRK11649
putative peptidase; Provisional
 14-217 9.25e-62

putative peptidase; Provisional


Pssm-ID: 236946 [Multi-domain]  Cd Length: 439  Bit Score: 199.89  E-value: 9.25e-62
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  14 SATRSGLESNEIATLQRSLPSRFNLRHLKKNESLKL-----VLQKKAGKSRVVAYKFTSGSFNYTAYRISDKKFYNLSDT 88
Cdd:PRK11649  198 SAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVlmsreMLDGKSEQSQLLGVRLRSGGKDYYAIRAEDGKFYDRNGS 277

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  89 S-GKGSLDYPLPATARLSSPFNPARLNPVSGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKT 167
Cdd:PRK11649  278 GlAKGFLRFPTAKQFRISSNFNPRRLNPVTGRVAPHRGVDFAMPVGTPVLAVGDGEVVVAKRSGAAGNYVAIRHGRQYTT 357

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 2126616135 168 RYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSL 217
Cdd:PRK11649  358 RYMHLRKLLVKPGQKVKRGDRIALSGNTGRSTGPHLHYEVWINQQAVNPL 407
NlpD COG0739
Murein DD-endopeptidase MepM and murein hydrolase activator NlpD, contains LysM domain [Cell ...
 95-219 1.79e-46

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: 153.20  E-value: 1.79e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  95 DYPLPATARLSSPFNPaRLNPVSGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNK 174
Cdd:COG0739    70 SGAWPVKGRITSGFGY-RRHPVTGRRRFHKGIDIAAPTGTPVYAAADGTVVFAGWNGGYGNLVIIDHGNGYTTLYAHLSS 148

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 2126616135 175 ILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSLAF 219
Cdd:COG0739   149 ILVKVGQRVKAGQVIGYVGNTGRSTGPHLHFEVRVNGKPVDPLPF 193
Peptidase_M23 pfam01551
Peptidase family M23; Members of this family are zinc metallopeptidases with a range of ...
 121-215 4.16e-35

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: 120.73  E-value: 4.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 121 SPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSG 200
Cdd:pfam01551   1 RFHKGIDIAAPTGTPVYAAADGVVVFAGWLGGYGNLVIIDHGNGYSTLYAHLSSILVKVGQRVKAGQVIGTVGSTGRSTG 80

                          90
                  ....*....|....*
gi 2126616135 201 PHLHYELVINNNPVN 215
Cdd:pfam01551  81 PHLHFEIRKNGKPVD 95
M23_peptidase cd12797
M23 family metallopeptidase, also known as beta-lytic metallopeptidase, and similar proteins; ...
 123-207 2.70e-34

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: 118.08  E-value: 2.70e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 123 HNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPH 202
Cdd:cd12797     1 HNGIDIAAPEGTPVYAAADGTVVFAGWDGGYGNYVIIDHGNGYYTLYAHLSSILVKVGQRVKKGQVIGTVGNTGRSTGPH 80


                  ....*
gi 2126616135 203 LHYEL 207
Cdd:cd12797    81 LHFEI 85
SpoIIQ2 COG5821
Stage II sporulation protein SpoIIQ, clostridial version, metallopeptidase M23 family [Cell ...
 73-219 1.68e-28

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: 107.03  E-value: 1.68e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  73 TAYRISDKKFYNLSDTSGKGSLDYPLPATARLSSPFNPARLNPVSGKVS-----------------PHNGIDYSMPMNTK 135
Cdd:COG5821    30 TAVWVTNNNLNKLEEETVKNKSESNEKSKSKVTASTSNKFLKPVSGKITrefgedlvysktlnewrTHTGIDIAAKEGTP 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 136 IVSVIDGKITRAEYNSTMGYFVEVTGKAGVKTRYLHLN-KILVTKGARVTRGDAIALSGNSGR---SSGPHLHYELVINN 211
Cdd:COG5821   110 VKAAADGVVVEVGKDPKYGITVVIDHGNGIKTVYANLDsKIKVKVGQKVKKGQVIGKVGSTALfesSEGPHLHFEVLKNG 189


                  ....*...
gi 2126616135 212 NPVNSLAF 219
Cdd:COG5821   190 KPVDPMKY 197
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 13-219 7.31e-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: 100.99  E-value: 7.31e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  13 LSATRSGLES--NEIATLQRSLPSRFN-----LRHLKKNE-SLKLVLQKKAGKSRVVAYKFTSGSFnytayrisdkkfyn 84
Cdd:COG4942   183 LEEERAALEAlkAERQKLLARLEKELAelaaeLAELQQEAeELEALIARLEAEAAAAAERTPAAGF-------------- 248

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  85 lsdTSGKGSLdyPLPATARLSSPFNPARlnpvsGKVSPHNGIDYSMPMNTKIVSVIDGKITRAEYNSTMGYFVEVTGKAG 164
Cdd:COG4942   249 ---AALKGKL--PWPVSGRVVRRFGERD-----GGGGRNKGIDIAAPPGAPVRAVADGTVVYAGWLRGYGNLVIIDHGGG 318

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2126616135 165 VKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNSLAF 219
Cdd:COG4942   319 YLTLYAHLSSLLVKVGQRVKAGQPIGTVGSSGGQGGPTLYFELRKNGKPVDPLPW 373
Csd3_N2 pfam19425
Csd3 second domain; This entry represents the second domain from the Csd3 peptidase. This ...
 14-110 6.65e-14

Csd3 second domain; This entry represents the second domain from the Csd3 peptidase. This domain has a similar structure to pfam18059 despite low sequence similarity.


Pssm-ID: 437257 [Multi-domain]  Cd Length: 122  Bit Score: 66.27  E-value: 6.65e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  14 SATRSGLESNEIATLQRSLPSRFNLRHLKKNESLKL-----VLQKKAGKSRVVAYKFTSGSFNYTAYRISDKKFYNLSDT 88
Cdd:pfam19425  20 SARKAGLTSNEISAVIKALQWQLDFRKLKKGDKFSVlmsreMLDGKREQSQLLGVRLRSGGKDYYAIRAEDGKFYDRNGS 99

                          90       100
                  ....*....|....*....|...
gi 2126616135  89 S-GKGSLDYPLPATARLSSPFNP 110
Cdd:pfam19425 100 GlARGFLRFPTAKQFRVSSNFNP 122
OapA COG3061
Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell ...
 62-238 7.54e-07

Cell division protein YtfB/OapA (opacity-associated protein A) [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 442295 [Multi-domain]  Cd Length: 425  Bit Score: 49.28  E-value: 7.54e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135  62 AYKFTSGSFNYTAYRISDKKFYNLSDTSGKGSLDYPLPATARLSSPFNPARLNPVSGKVSPHNGIDYSMPMNTKIVSVID 141
Cdd:COG3061   249 AKFRRRAVRFRRSSSSSSYRRRPHRLSRRRRLRRGPDAAAPSGSSNAAGGGGHKITRRGGGGGGAAVGVGTGTPTTGAGL 328

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2126616135 142 GKITRAEYNSTMGYFVEVTGKAGVKTRYLHLNKILVTKGARVTRGDAIALSGNSGRSSGPHLHYELVINNNPVNsLAFRT 221
Cdd:COG3061   329 GVVRGGRGGGGGVVVGQIGRGGTYGGTGLHLHKHGHKGGGVVGQGVTIGTLGGTGPTTGPHLHYEFVQNGVRVA-PLTVK 407

                         170
                  ....*....|....*..
gi 2126616135 222 AAPADNKLEQHAFAHAR 238
Cdd:COG3061   408 LPAAPPLAAAAAAAFKA 424
 
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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