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Conserved domains on  [gi|872701488|ref|WP_048553142|]
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MULTISPECIES: L,D-transpeptidase [Bacillus]

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];
31-152 5.62e-40

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


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 130.75  E-value: 5.62e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  31 LIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNrPYYTG-----KIKGGDPRNPLGDRWLGLnmagt 105
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAEN-PTWTPpaempAGMPGGPDNPLGPYALYL----- 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 872701488 106 YGTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:COG1376   75 SDGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
31-152 5.62e-40

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 130.75  E-value: 5.62e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  31 LIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNrPYYTG-----KIKGGDPRNPLGDRWLGLnmagt 105
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAEN-PTWTPpaempAGMPGGPDNPLGPYALYL----- 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 872701488 106 YGTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:COG1376   75 SDGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 31-152 9.18e-37

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: 122.42  E-value: 9.18e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  31 LIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNRPYYTGKIKGGDPRNPLGDRWLGLNmagTYGTTY 110
Cdd:cd16913    2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLGPYALRLS---GPGSGI 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 872701488 111 AIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:cd16913   79 GIHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 31-152 2.17e-13

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: 61.60  E-value: 2.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488   31 LIVN-TQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIvnkiknrpyytgkikggdprnplgdrwlglnmagtygtt 109
Cdd:pfam03734   4 IVVDlSEQRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRI--------------------------------------- 44

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 872701488  110 YAIHGTN--NNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:pfam03734  45 IYIHDTGtpDLFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 14-145 1.12e-12

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 63.90  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  14 VLTIPFTNAEAATTKDQLIVNTQLNKMDYYQNG-KFIKSFTVATGKAATPTPKGTFQIVNKIKNRPYYTGKIK------- 85
Cdd:PRK10260  84 VLNIPQQLILPDTVHEGIVINSAEMRLYYYPKGtNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKmhaeyra 163

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 872701488  86 GGDPRN---PLG-DRWLGLnMAGTYGTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIP 145
Cdd:PRK10260 164 AGEPLPavvPAGpDNPMGL-YALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVP 226
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
31-152 5.62e-40

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 130.75  E-value: 5.62e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  31 LIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNrPYYTG-----KIKGGDPRNPLGDRWLGLnmagt 105
Cdd:COG1376    1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKAEN-PTWTPpaempAGMPGGPDNPLGPYALYL----- 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 872701488 106 YGTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:COG1376   75 SDGGYGIHGTPWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 31-152 9.18e-37

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: 122.42  E-value: 9.18e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  31 LIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNRPYYTGKIKGGDPRNPLGDRWLGLNmagTYGTTY 110
Cdd:cd16913    2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLGPYALRLS---GPGSGI 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 872701488 111 AIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:cd16913   79 GIHGTPWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVI 120
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 31-152 2.17e-13

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: 61.60  E-value: 2.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488   31 LIVN-TQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIvnkiknrpyytgkikggdprnplgdrwlglnmagtygtt 109
Cdd:pfam03734   4 IVVDlSEQRLLYLYENGGLVLRYPVSVGRGDGPTPTGTFRI--------------------------------------- 44

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 872701488  110 YAIHGTN--NNQAIGKWTTLGCIRMYNNDIHWLFERIPQQATVTV 152
Cdd:pfam03734  45 IYIHDTGtpDLFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PRK10260 PRK10260
L,D-transpeptidase; Provisional
 14-145 1.12e-12

L,D-transpeptidase; Provisional


Pssm-ID: 182341 [Multi-domain]  Cd Length: 306  Bit Score: 63.90  E-value: 1.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  14 VLTIPFTNAEAATTKDQLIVNTQLNKMDYYQNG-KFIKSFTVATGKAATPTPKGTFQIVNKIKNRPYYTGKIK------- 85
Cdd:PRK10260  84 VLNIPQQLILPDTVHEGIVINSAEMRLYYYPKGtNTVIVLPIGIGQLGKDTPINWTTKVERKKAGPTWTPTAKmhaeyra 163

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 872701488  86 GGDPRN---PLG-DRWLGLnMAGTYGTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIP 145
Cdd:PRK10260 164 AGEPLPavvPAGpDNPMGL-YALYIGRLYAIHGTNANFGIGLRVSHGCVRLRNEDIKFLFEKVP 226
PRK10190 PRK10190
L,D-transpeptidase; Provisional
 15-145 2.46e-12

L,D-transpeptidase; Provisional


Pssm-ID: 182294 [Multi-domain]  Cd Length: 310  Bit Score: 62.96  E-value: 2.46e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  15 LTIPFTNAEAATTKDQLIVNTQLNKMDYY-QNGKFIKSFTVATGKAATPTPKGTFQIVNKIKNRPYYT------------ 81
Cdd:PRK10190  82 LTIPQQLILPDTVRKGIVVNVAEMRLYYYpPDSNTVEVFPIGIGQAGRETPRNWVTTVERKQEAPTWTptpntrreyakr 161

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 872701488  82 GK-----IKGGdPRNPLGdrwlglnMAGTY-GTTYAIHGTNNNQAIGKWTTLGCIRMYNNDIHWLFERIP 145
Cdd:PRK10190 162 GEslpafVPAG-PDNPMG-------LYAIYiGRLYAIHGTNANFGIGLRVSQGCIRLRNDDIKYLFDNVP 223
PRK06132 PRK06132
hypothetical protein; Provisional
 30-75 2.72e-03

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 36.96  E-value: 2.72e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 872701488  30 QLIVNTQLNKMDYYQNGKFIKSFTVATGKAATPTPKGTFQIVNKIK 75
Cdd:PRK06132  62 VIVVSLDEQRLYVYDNGILIAVSTVSTGKRGHETPTGVFSILQKDK 107
 
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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