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Conserved domains on  [gi|1426249746|ref|WP_113135458|]
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murein L,D-transpeptidase family protein [Ensifer sp. ENS08]

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
YafK COG3034
Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];
1-162 2.05e-64

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


:

Pssm-ID: 442269 [Multi-domain]  Cd Length: 163  Bit Score: 194.37  E-value: 2.05e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746   1 MRLALVAATLVASGGFPAA--AADSADRVVVHNERRLLQLFQGD----QVIRKYTIALGGNPIGHKRQEGDQRTPEGLYS 74
Cdd:COG3034     2 MRLLLLLALLALAALLPPAllSPPSPVLIVVDKSERRLELWKGDdgrgKLLKTYPICLGSGPLGPKRREGDRRTPEGFYF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  75 LDWRNPGSGYYKSIHVSYPapadvsaaaaN--------GVDPGGMIMIHGQPNYfgwlaFLTQCFDWTNGCIAVTNAEME 146
Cdd:COG3034    82 ITRRNPNSKYHLAFGISYP----------NaydrargrGRSTGGGIMIHGTPSG-----DYHRPPDWTDGCIALTNEDIE 146

                         170
                  ....*....|....*..
gi 1426249746 147 EIWAMVP-NNTPIEIKP 162
Cdd:COG3034   147 EIYALVReDGTPVVIFP 163
 
Name Accession Description Interval E-value
YafK COG3034
Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];
1-162 2.05e-64

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


Pssm-ID: 442269 [Multi-domain]  Cd Length: 163  Bit Score: 194.37  E-value: 2.05e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746   1 MRLALVAATLVASGGFPAA--AADSADRVVVHNERRLLQLFQGD----QVIRKYTIALGGNPIGHKRQEGDQRTPEGLYS 74
Cdd:COG3034     2 MRLLLLLALLALAALLPPAllSPPSPVLIVVDKSERRLELWKGDdgrgKLLKTYPICLGSGPLGPKRREGDRRTPEGFYF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  75 LDWRNPGSGYYKSIHVSYPapadvsaaaaN--------GVDPGGMIMIHGQPNYfgwlaFLTQCFDWTNGCIAVTNAEME 146
Cdd:COG3034    82 ITRRNPNSKYHLAFGISYP----------NaydrargrGRSTGGGIMIHGTPSG-----DYHRPPDWTDGCIALTNEDIE 146

                         170
                  ....*....|....*..
gi 1426249746 147 EIWAMVP-NNTPIEIKP 162
Cdd:COG3034   147 EIYALVReDGTPVVIFP 163
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 26-160 4.81e-18

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: 75.04  E-value: 4.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  26 RVVVHNERRLLQLFQGDQVIRKYTIALGGNpighkrqegDQRTPEGLYSLDW--RNPGSGYYKSIHVSYPAPADVSAAAA 103
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKP---------GTPTPTGTFRITRkvKNPTWTGPPSIPPGPYNPLGPYALRL 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1426249746 104 NGvdPGGMIMIHG--QPNYFGWlafltqcfDWTNGCIAVTNAEMEEIWAMVPNNTPIEI 160
Cdd:cd16913    72 SG--PGSGIGIHGtpWPSSIGR--------PASHGCIRLSNEDAKELYDWVPVGTPVVI 120
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 25-160 4.55e-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: 55.82  E-value: 4.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  25 DRVVVH-NERRLLQLFQGDQVIRKYTIALGgnpighkrqEGDQRTPEGLYSldwrnpgsgyyksihvsypapadvsaaaa 103
Cdd:pfam03734   2 RYIVVDlSEQRLLYLYENGGLVLRYPVSVG---------RGDGPTPTGTFR----------------------------- 43

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1426249746 104 ngvdpggMIMIHGQPNYFGWLAFltqcFDWTNGCIAVTNAEMEEIWAMVPNNTPIEI 160
Cdd:pfam03734  44 -------IIYIHDTGTPDLFGLG----RRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
 
Name Accession Description Interval E-value
YafK COG3034
Murein L,D-transpeptidase YafK [Cell wall/membrane/envelope biogenesis];
1-162 2.05e-64

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


Pssm-ID: 442269 [Multi-domain]  Cd Length: 163  Bit Score: 194.37  E-value: 2.05e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746   1 MRLALVAATLVASGGFPAA--AADSADRVVVHNERRLLQLFQGD----QVIRKYTIALGGNPIGHKRQEGDQRTPEGLYS 74
Cdd:COG3034     2 MRLLLLLALLALAALLPPAllSPPSPVLIVVDKSERRLELWKGDdgrgKLLKTYPICLGSGPLGPKRREGDRRTPEGFYF 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  75 LDWRNPGSGYYKSIHVSYPapadvsaaaaN--------GVDPGGMIMIHGQPNYfgwlaFLTQCFDWTNGCIAVTNAEME 146
Cdd:COG3034    82 ITRRNPNSKYHLAFGISYP----------NaydrargrGRSTGGGIMIHGTPSG-----DYHRPPDWTDGCIALTNEDIE 146

                         170
                  ....*....|....*..
gi 1426249746 147 EIWAMVP-NNTPIEIKP 162
Cdd:COG3034   147 EIYALVReDGTPVVIFP 163
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 26-160 4.81e-18

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: 75.04  E-value: 4.81e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  26 RVVVHNERRLLQLFQGDQVIRKYTIALGGNpighkrqegDQRTPEGLYSLDW--RNPGSGYYKSIHVSYPAPADVSAAAA 103
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKP---------GTPTPTGTFRITRkvKNPTWTGPPSIPPGPYNPLGPYALRL 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1426249746 104 NGvdPGGMIMIHG--QPNYFGWlafltqcfDWTNGCIAVTNAEMEEIWAMVPNNTPIEI 160
Cdd:cd16913    72 SG--PGSGIGIHGtpWPSSIGR--------PASHGCIRLSNEDAKELYDWVPVGTPVVI 120
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 25-160 4.55e-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: 55.82  E-value: 4.55e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1426249746  25 DRVVVH-NERRLLQLFQGDQVIRKYTIALGgnpighkrqEGDQRTPEGLYSldwrnpgsgyyksihvsypapadvsaaaa 103
Cdd:pfam03734   2 RYIVVDlSEQRLLYLYENGGLVLRYPVSVG---------RGDGPTPTGTFR----------------------------- 43

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1426249746 104 ngvdpggMIMIHGQPNYFGWLAFltqcFDWTNGCIAVTNAEMEEIWAMVPNNTPIEI 160
Cdd:pfam03734  44 -------IIYIHDTGTPDLFGLG----RRRSHGCIRLSNEDAKELYDRVLVGTPVVI 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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