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Conserved domains on  [gi|2564843625|ref|WP_306047204|]
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L,D-transpeptidase [Nioella sp. MMSF_3534]

Protein Classification

L,D-transpeptidase( domain architecture ID 11443278)

L,D-transpeptidase catalyzes the formation of 3--3 peptidoglycan cross-links

CATH:  2.40.440.10
EC:  2.-.-.-
Gene Ontology:  GO:0018104|GO:0071972|GO:0042834
PubMed:  18266857
SCOP:  4000465|4002015

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
72-201 8.00e-45

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 145.39  E-value: 8.00e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHIQDDGTAMRYGVAIGRNDLYEP-GTYTVGRKARWPSWTPTANMiarepgvyeqyADGMPGGPENPLGA 150
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPtGTFRVLRKAENPTWTPPAEM-----------PAGMPGGPDNPLGP 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 151 RALYLYvgnrDTYLRIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:COG1376    70 YALYLS----DGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVG 116
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
72-201 8.00e-45

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 145.39  E-value: 8.00e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHIQDDGTAMRYGVAIGRNDLYEP-GTYTVGRKARWPSWTPTANMiarepgvyeqyADGMPGGPENPLGA 150
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPtGTFRVLRKAENPTWTPPAEM-----------PAGMPGGPDNPLGP 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 151 RALYLYvgnrDTYLRIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:COG1376    70 YALYLS----DGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVG 116
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 72-201 1.94e-27

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.


Pssm-ID: 341130 [Multi-domain]  Cd Length: 121  Bit Score: 100.85  E-value: 1.94e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHIQDDGTAMRYGVAIGRNDLYEP-GTYTVGRKARWPSWTPTanmiarepgvyeqyaDGMPGGPENPLGA 150
Cdd:cd16913     2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPtGTFRITRKVKNPTWTGP---------------PSIPPGPYNPLGP 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 151 RALYLYVGNRDTYlrIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:cd16913    67 YALRLSGPGSGIG--IHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVG 115
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 76-201 9.71e-17

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 77.00  E-value: 9.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  76 AVARYLYHIQDDGTAMRYGVAIGRNDLYEPGTYT--VGRKARWPSWTPTANMIAREPGVYEQYADGMPGGPENPLGARAL 153
Cdd:PRK10260  106 AEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTtkVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYAL 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 154 Y---LYVgnrdtylrIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:PRK10260  186 YigrLYA--------IHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVG 228
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 72-201 3.91e-08

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.


Pssm-ID: 461031 [Multi-domain]  Cd Length: 89  Bit Score: 49.27  E-value: 3.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHI-QDDGTAMRYGVAIGRNDlyepgtytvgrkarwpSWTPTanmiarepGVYEQYAdgmpggpenplga 150
Cdd:pfam03734   4 IVVDLSEQRLLYLyENGGLVLRYPVSVGRGD----------------GPTPT--------GTFRIIY------------- 46

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2564843625 151 ralylyvgnrdtylrIHGTPQPW--SIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:pfam03734  47 ---------------IHDTGTPDlfGLGRRRSHGCIRLSNEDAKELYDRVLVG 84
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
72-201 8.00e-45

Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 145.39  E-value: 8.00e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHIQDDGTAMRYGVAIGRNDLYEP-GTYTVGRKARWPSWTPTANMiarepgvyeqyADGMPGGPENPLGA 150
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPtGTFRVLRKAENPTWTPPAEM-----------PAGMPGGPDNPLGP 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 151 RALYLYvgnrDTYLRIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:COG1376    70 YALYLS----DGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVG 116
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 72-201 1.94e-27

L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like family of proteins are found in a range of bacteria. The best studied member Bacillus YkuD has been shown to act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. Another member Helicobacter pylori Csd6 functions as an L,D-carboxypeptidase and regulates helical cell shape and motility. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue.


Pssm-ID: 341130 [Multi-domain]  Cd Length: 121  Bit Score: 100.85  E-value: 1.94e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHIQDDGTAMRYGVAIGRNDLYEP-GTYTVGRKARWPSWTPTanmiarepgvyeqyaDGMPGGPENPLGA 150
Cdd:cd16913     2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPtGTFRITRKVKNPTWTGP---------------PSIPPGPYNPLGP 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 151 RALYLYVGNRDTYlrIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:cd16913    67 YALRLSGPGSGIG--IHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVG 115
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 76-201 9.71e-17

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 77.00  E-value: 9.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  76 AVARYLYHIQDDGTAMRYGVAIGRNDLYEPGTYT--VGRKARWPSWTPTANMIAREPGVYEQYADGMPGGPENPLGARAL 153
Cdd:PRK10260  106 AEMRLYYYPKGTNTVIVLPIGIGQLGKDTPINWTtkVERKKAGPTWTPTAKMHAEYRAAGEPLPAVVPAGPDNPMGLYAL 185

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 154 Y---LYVgnrdtylrIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:PRK10260  186 YigrLYA--------IHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVG 228
PRK10190 PRK10190
L,D-transpeptidase; Provisional
 76-201 1.46e-12

L,D-transpeptidase; Provisional


Pssm-ID: 182294 [Multi-domain]  Cd Length: 310  Bit Score: 65.27  E-value: 1.46e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  76 AVARYLYHIQDDGTAMRYGVAIGRNDLYEPGTY--TVGRKARWPSWTPTANMIAREPGVYEQYADGMPGGPENPLGARAL 153
Cdd:PRK10190  103 AEMRLYYYPPDSNTVEVFPIGIGQAGRETPRNWvtTVERKQEAPTWTPTPNTRREYAKRGESLPAFVPAGPDNPMGLYAI 182

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2564843625 154 Y---LYVgnrdtylrIHGTPQPWSIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:PRK10190  183 YigrLYA--------IHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVG 225
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 72-201 3.91e-08

L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. It has been shown that this domain can act as an L,D-transpeptidase that gives rise to an alternative pathway for peptidoglycan cross-linking. This gives bacteria resistance to beta-lactam antibiotics that inhibit PBPs which usually carry out the cross-linking reaction. The conserved region contains a conserved histidine and cysteine, with the cysteine thought to be an active site residue. Several members of this family contain peptidoglycan binding domains. The molecular structure of YkuD protein shows this domain has a novel tertiary fold consisting of a beta-sandwich with two mixed sheets, one containing five strands and the other, six strands. The two beta-sheets form a cradle capped by an alpha-helix. This family was formerly called the ErfK/YbiS/YcfS/YnhG family, but is now named after the first protein of known structure.


Pssm-ID: 461031 [Multi-domain]  Cd Length: 89  Bit Score: 49.27  E-value: 3.91e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2564843625  72 IHVDAVARYLYHI-QDDGTAMRYGVAIGRNDlyepgtytvgrkarwpSWTPTanmiarepGVYEQYAdgmpggpenplga 150
Cdd:pfam03734   4 IVVDLSEQRLLYLyENGGLVLRYPVSVGRGD----------------GPTPT--------GTFRIIY------------- 46

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2564843625 151 ralylyvgnrdtylrIHGTPQPW--SIGRRASSGCVRMVMAHIIGLYDNVDVG 201
Cdd:pfam03734  47 ---------------IHDTGTPDlfGLGRRRSHGCIRLSNEDAKELYDRVLVG 84
 
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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