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Conserved domains on  [gi|750096734|ref|WP_040401417|]
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L,D-transpeptidase [Amorphus coralli]

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];
76-209 3.62e-52

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


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 164.26  E-value: 3.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIRYGVGVGREGFG-WSGEVEVGRKAEWPTWTPPAEMierdpdsakyAGGMPGGPDNPLGAR 154
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPtPTGTFRVLRKAENPTWTPPAEM----------PAGMPGGPDNPLGPY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 750096734 155 ALYLYKDGrdslYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:COG1376   71 ALYLSDGG----YGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
76-209 3.62e-52

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 164.26  E-value: 3.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIRYGVGVGREGFG-WSGEVEVGRKAEWPTWTPPAEMierdpdsakyAGGMPGGPDNPLGAR 154
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPtPTGTFRVLRKAENPTWTPPAEM----------PAGMPGGPDNPLGPY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 750096734 155 ALYLYKDGrdslYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:COG1376   71 ALYLSDGG----YGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 76-209 1.62e-29

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: 106.24  E-value: 1.62e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIRYGVGVGREGFG-WSGEVEVGRKAEWPTWTPPaemierdpdsakyaGGMPGGPDNPLGAR 154
Cdd:cd16913    2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPtPTGTFRITRKVKNPTWTGP--------------PSIPPGPYNPLGPY 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 750096734 155 ALYLYKDGRDslYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:cd16913   68 ALRLSGPGSG--IGIHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 76-207 1.63e-23

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 95.48  E-value: 1.63e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFY---------VLPdfqairygVGVGREG----FGWSGEVEvgRKAEWPTWTPPAEMierdpdSAKYAGG 142
Cdd:PRK10260 101 IVINSAEMRLYYypkgtntviVLP--------IGIGQLGkdtpINWTTKVE--RKKAGPTWTPTAKM------HAEYRAA 164

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 750096734 143 -------MPGGPDNPLGARALYLykdGRdsLYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKV 207
Cdd:PRK10260 165 geplpavVPAGPDNPMGLYALYI---GR--LYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRV 231
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 162-209 7.87e-11

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: 56.59  E-value: 7.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 750096734  162 GRDSLYRVHGTNEPW--SIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:pfam03734  40 GTFRIIYIHDTGTPDlfGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
76-209 3.62e-52

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 164.26  E-value: 3.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIRYGVGVGREGFG-WSGEVEVGRKAEWPTWTPPAEMierdpdsakyAGGMPGGPDNPLGAR 154
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPtPTGTFRVLRKAENPTWTPPAEM----------PAGMPGGPDNPLGPY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 750096734 155 ALYLYKDGrdslYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:COG1376   71 ALYLSDGG----YGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 76-209 1.62e-29

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: 106.24  E-value: 1.62e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIRYGVGVGREGFG-WSGEVEVGRKAEWPTWTPPaemierdpdsakyaGGMPGGPDNPLGAR 154
Cdd:cd16913    2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPtPTGTFRITRKVKNPTWTGP--------------PSIPPGPYNPLGPY 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 750096734 155 ALYLYKDGRDslYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:cd16913   68 ALRLSGPGSG--IGIHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 76-207 1.63e-23

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 95.48  E-value: 1.63e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFY---------VLPdfqairygVGVGREG----FGWSGEVEvgRKAEWPTWTPPAEMierdpdSAKYAGG 142
Cdd:PRK10260 101 IVINSAEMRLYYypkgtntviVLP--------IGIGQLGkdtpINWTTKVE--RKKAGPTWTPTAKM------HAEYRAA 164

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 750096734 143 -------MPGGPDNPLGARALYLykdGRdsLYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKV 207
Cdd:PRK10260 165 geplpavVPAGPDNPMGLYALYI---GR--LYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVPVGTRV 231
PRK10190 PRK10190
L,D-transpeptidase; Provisional
 76-212 1.95e-18

L,D-transpeptidase; Provisional


Pssm-ID: 182294 [Multi-domain]  Cd Length: 310  Bit Score: 81.84  E-value: 1.95e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 750096734  76 IIIDTDRKYLFYVLPDFQAIR-YGVGVGREGF----GWSGEVEvgRKAEWPTWTPPAEMIERDPDSAKYAGGM-PGGPDN 149
Cdd:PRK10190  98 IVVNVAEMRLYYYPPDSNTVEvFPIGIGQAGRetprNWVTTVE--RKQEAPTWTPTPNTRREYAKRGESLPAFvPAGPDN 175

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 750096734 150 PLGARALYLykdGRdsLYRVHGTNEPWSIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIVLKQ 212
Cdd:PRK10190 176 PMGLYAIYI---GR--LYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVPVGTRVQIIDQ 233
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 162-209 7.87e-11

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: 56.59  E-value: 7.87e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 750096734  162 GRDSLYRVHGTNEPW--SIGHSVSSGCIRMNNEDVIDLYSRTEPGTKVIV 209
Cdd:pfam03734  40 GTFRIIYIHDTGTPDlfGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
 
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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