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Conserved domains on  [gi|1103740387|ref|WP_071696382|]
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MULTISPECIES: peptidoglycan meso-diaminopimelic acid protein amidase [Citrobacter]

Protein Classification

L,D-transpeptidase family protein( domain architecture ID 10789902)

L,D-transpeptidase family protein similar to Campylobacter jejuni LD-carboxypeptidase Pgp2 that cleaves D-Ala from both monomeric and cross-linked tetrapeptides

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LdtF_DpaA_YafK NF040599
peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein ...
 1-246 3.41e-166

peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein L,D-transpeptidases, but actually functions as an amidase. In E. coli, the most abundant protein is the lipoprotein Lpp, anchored to the inner face of the outer membrane, but cross-linked to the peptidoglycan cell wall by the transpeptidases LdtA, LdtB, and LdtC. DpaA (peptidoglycan meso-diaminopimelic acid protein amidase A) is an amidase that hydrolyzes those linkages.


:

Pssm-ID: 468573  Cd Length: 242  Bit Score: 458.70  E-value: 3.41e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387   1 MRKIAFFLAMLL-LPCVSFAGLLSSSSPTTPvsKEYKQQLMGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICNYSGG 79
Cdd:NF040599    1 MGKIALLLAMLFsLPAVSFASSSASEVVPVA--PVSKQQLLGSPVYIQIFKEERTLELYAKIGNEYRLLDSYRICNFSGG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  80 LGPKQRQGDFKSPEGFYSVQRGQLKPDSRFYKAINIGFPNAYDRAHGYEGKYLMIHGACVSVGCYAMTDNGIDEIFQFVT 159
Cdd:NF040599   79 LGPKRREGDFKSPEGFYSVDLRQLKPDSRFYRAINIGFPNEYDRAQGYSGKYLMIHGDCVSIGCYAMTDAYMDEIYQYVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387 160 GALVFGQSSVQVSIYPFRMTDANMQRHKFSYYKDFWTQLKPGYDYFEQTRKPPTVSVVDGRYVVSKPLsheVVQPQLASN 239
Cdd:NF040599  159 AALRNGQPRVEVSIYPFRMTDQNMQRHRNSSYINFWRQLQPGYAYFVQNHQPPAVSVNNGQYVVNQPS---LAASQLASN 235


                  ....*..
gi 1103740387 240 YTLPETK 246
Cdd:NF040599  236 LALTEAK 242
 
Name Accession Description Interval E-value
LdtF_DpaA_YafK NF040599
peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein ...
 1-246 3.41e-166

peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein L,D-transpeptidases, but actually functions as an amidase. In E. coli, the most abundant protein is the lipoprotein Lpp, anchored to the inner face of the outer membrane, but cross-linked to the peptidoglycan cell wall by the transpeptidases LdtA, LdtB, and LdtC. DpaA (peptidoglycan meso-diaminopimelic acid protein amidase A) is an amidase that hydrolyzes those linkages.


Pssm-ID: 468573  Cd Length: 242  Bit Score: 458.70  E-value: 3.41e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387   1 MRKIAFFLAMLL-LPCVSFAGLLSSSSPTTPvsKEYKQQLMGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICNYSGG 79
Cdd:NF040599    1 MGKIALLLAMLFsLPAVSFASSSASEVVPVA--PVSKQQLLGSPVYIQIFKEERTLELYAKIGNEYRLLDSYRICNFSGG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  80 LGPKQRQGDFKSPEGFYSVQRGQLKPDSRFYKAINIGFPNAYDRAHGYEGKYLMIHGACVSVGCYAMTDNGIDEIFQFVT 159
Cdd:NF040599   79 LGPKRREGDFKSPEGFYSVDLRQLKPDSRFYRAINIGFPNEYDRAQGYSGKYLMIHGDCVSIGCYAMTDAYMDEIYQYVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387 160 GALVFGQSSVQVSIYPFRMTDANMQRHKFSYYKDFWTQLKPGYDYFEQTRKPPTVSVVDGRYVVSKPLsheVVQPQLASN 239
Cdd:NF040599  159 AALRNGQPRVEVSIYPFRMTDQNMQRHRNSSYINFWRQLQPGYAYFVQNHQPPAVSVNNGQYVVNQPS---LAASQLASN 235


                  ....*..
gi 1103740387 240 YTLPETK 246
Cdd:NF040599  236 LALTEAK 242
YafK COG3034
Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];
1-175 3.07e-60

Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442269 [Multi-domain]  Cd Length: 163  Bit Score: 187.05  E-value: 3.07e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387   1 MRKIAFFLAMLLLPCVSFAGLLSSsspttpvskeykqqlmGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICNYSGGL 80
Cdd:COG3034     1 MMRLLLLLALLALAALLPPALLSP----------------PSPVLIVVDKSERRLELWKGDDGRGKLLKTYPICLGSGPL 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  81 GPKQRQGDFKSPEGFYSVQRgqLKPDSRFYKAINIGFPNAYDRAHGYE---GKYLMIHGACV---------SVGCYAMTD 148
Cdd:COG3034    65 GPKRREGDRRTPEGFYFITR--RNPNSKYHLAFGISYPNAYDRARGRGrstGGGIMIHGTPSgdyhrppdwTDGCIALTN 142

                         170       180
                  ....*....|....*....|....*..
gi 1103740387 149 NGIDEIFQFVTgalvfgQSSVQVSIYP 175
Cdd:COG3034   143 EDIEEIYALVR------EDGTPVVIFP 163
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 45-158 2.94e-07

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: 48.07  E-value: 2.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  45 YIQIFKEERTLDLYvkmgEQYQLLDSYKIcnySGGlgpkqrQGDFKSPEGFYSVQRGQLKPDSRFYKAINIGFPNAY-DR 123
Cdd:cd16913     1 YIVVDLSEQRLYLY----ENGKLVKTYPV---STG------KPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLgPY 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1103740387 124 AHG--YEGKYLMIHGAC--------VSVGCYAMTDNGIDEIFQFV 158
Cdd:cd16913    68 ALRlsGPGSGIGIHGTPwpssigrpASHGCIRLSNEDAKELYDWV 112
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 43-164 2.16e-03

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: 36.17  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  43 PVYIQIFKEERTLDLYVKMGeqyQLLDSYKICnysggLGPkqrqGDFKSPEGFYSVqrgqlkpdsrfykainIGFpnayd 122
Cdd:pfam03734   1 DRYIVVDLSEQRLLYLYENG---GLVLRYPVS-----VGR----GDGPTPTGTFRI----------------IYI----- 47

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1103740387 123 raHGYEGKYLMIHGACVSVGCYAMTDNGIDEIFQFVT-GALVF 164
Cdd:pfam03734  48 --HDTGTPDLFGLGRRRSHGCIRLSNEDAKELYDRVLvGTPVV 88
 
Name Accession Description Interval E-value
LdtF_DpaA_YafK NF040599
peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein ...
 1-246 3.41e-166

peptidoglycan meso-diaminopimelic acid protein amidase; DpaA (previously YafK and LdtF) murein L,D-transpeptidases, but actually functions as an amidase. In E. coli, the most abundant protein is the lipoprotein Lpp, anchored to the inner face of the outer membrane, but cross-linked to the peptidoglycan cell wall by the transpeptidases LdtA, LdtB, and LdtC. DpaA (peptidoglycan meso-diaminopimelic acid protein amidase A) is an amidase that hydrolyzes those linkages.


Pssm-ID: 468573  Cd Length: 242  Bit Score: 458.70  E-value: 3.41e-166
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387   1 MRKIAFFLAMLL-LPCVSFAGLLSSSSPTTPvsKEYKQQLMGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICNYSGG 79
Cdd:NF040599    1 MGKIALLLAMLFsLPAVSFASSSASEVVPVA--PVSKQQLLGSPVYIQIFKEERTLELYAKIGNEYRLLDSYRICNFSGG 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  80 LGPKQRQGDFKSPEGFYSVQRGQLKPDSRFYKAINIGFPNAYDRAHGYEGKYLMIHGACVSVGCYAMTDNGIDEIFQFVT 159
Cdd:NF040599   79 LGPKRREGDFKSPEGFYSVDLRQLKPDSRFYRAINIGFPNEYDRAQGYSGKYLMIHGDCVSIGCYAMTDAYMDEIYQYVE 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387 160 GALVFGQSSVQVSIYPFRMTDANMQRHKFSYYKDFWTQLKPGYDYFEQTRKPPTVSVVDGRYVVSKPLsheVVQPQLASN 239
Cdd:NF040599  159 AALRNGQPRVEVSIYPFRMTDQNMQRHRNSSYINFWRQLQPGYAYFVQNHQPPAVSVNNGQYVVNQPS---LAASQLASN 235


                  ....*..
gi 1103740387 240 YTLPETK 246
Cdd:NF040599  236 LALTEAK 242
YafK COG3034
Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];
1-175 3.07e-60

Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442269 [Multi-domain]  Cd Length: 163  Bit Score: 187.05  E-value: 3.07e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387   1 MRKIAFFLAMLLLPCVSFAGLLSSsspttpvskeykqqlmGSPVYIQIFKEERTLDLYVKMGEQYQLLDSYKICNYSGGL 80
Cdd:COG3034     1 MMRLLLLLALLALAALLPPALLSP----------------PSPVLIVVDKSERRLELWKGDDGRGKLLKTYPICLGSGPL 64

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  81 GPKQRQGDFKSPEGFYSVQRgqLKPDSRFYKAINIGFPNAYDRAHGYE---GKYLMIHGACV---------SVGCYAMTD 148
Cdd:COG3034    65 GPKRREGDRRTPEGFYFITR--RNPNSKYHLAFGISYPNAYDRARGRGrstGGGIMIHGTPSgdyhrppdwTDGCIALTN 142

                         170       180
                  ....*....|....*....|....*..
gi 1103740387 149 NGIDEIFQFVTgalvfgQSSVQVSIYP 175
Cdd:COG3034   143 EDIEEIYALVR------EDGTPVVIFP 163
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 45-158 2.94e-07

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: 48.07  E-value: 2.94e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  45 YIQIFKEERTLDLYvkmgEQYQLLDSYKIcnySGGlgpkqrQGDFKSPEGFYSVQRGQLKPDSRFYKAINIGFPNAY-DR 123
Cdd:cd16913     1 YIVVDLSEQRLYLY----ENGKLVKTYPV---STG------KPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLgPY 67

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1103740387 124 AHG--YEGKYLMIHGAC--------VSVGCYAMTDNGIDEIFQFV 158
Cdd:cd16913    68 ALRlsGPGSGIGIHGTPwpssigrpASHGCIRLSNEDAKELYDWV 112
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 43-164 2.16e-03

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: 36.17  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103740387  43 PVYIQIFKEERTLDLYVKMGeqyQLLDSYKICnysggLGPkqrqGDFKSPEGFYSVqrgqlkpdsrfykainIGFpnayd 122
Cdd:pfam03734   1 DRYIVVDLSEQRLLYLYENG---GLVLRYPVS-----VGR----GDGPTPTGTFRI----------------IYI----- 47

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1103740387 123 raHGYEGKYLMIHGACVSVGCYAMTDNGIDEIFQFVT-GALVF 164
Cdd:pfam03734  48 --HDTGTPDLFGLGRRRSHGCIRLSNEDAKELYDRVLvGTPVV 88
 
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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