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Conserved domains on  [gi|1081285178|gb|OFU26165|]
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hypothetical protein HMPREF3077_00050 [Clostridium sp. HMSC19C05]

Protein Classification

L,D-transpeptidase( domain architecture ID 13014342)

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

CATH:  2.40.440.10
EC:  2.-.-.-
Gene Ontology:  GO:0071972|GO:0042834
SCOP:  4002015

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 17-136 2.41e-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: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  17 LIVTDLRNKYTYIFKKDNggwgQLYKWQCTIGKPETPTITGIFYISGRKPSFGTDEYSVKYATRIKGGYYYHSVLYDSTG 96
Cdd:cd16913     1 YIVVDLSEQRLYLYENGK----LVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLGPYALRLSGPGS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1081285178  97 SYII-----DGRLGEALSHGCIRLSTENAKWIYDNIPDTTTVIIH 136
Cdd:cd16913    77 GIGIhgtpwPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 17-136 2.41e-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: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  17 LIVTDLRNKYTYIFKKDNggwgQLYKWQCTIGKPETPTITGIFYISGRKPSFGTDEYSVKYATRIKGGYYYHSVLYDSTG 96
Cdd:cd16913     1 YIVVDLSEQRLYLYENGK----LVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLGPYALRLSGPGS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1081285178  97 SYII-----DGRLGEALSHGCIRLSTENAKWIYDNIPDTTTVIIH 136
Cdd:cd16913    77 GIGIhgtpwPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
18-135 8.85e-16

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 68.35  E-value: 8.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  18 IVTDLRNKYTYIFKKDnggwGQLYKWQCTIGKPETPTITGIFYISGRKP---SFGTDEYSV-----------KYATRIKG 83
Cdd:COG1376     1 IVVDLSEQRLYVYEDG----GLVRTYPVSVGRPGFPTPTGTFRVLRKAEnptWTPPAEMPAgmpggpdnplgPYALYLSD 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1081285178  84 GYYY-HsvlydstGSYIIDGrLGEALSHGCIRLSTENAKWIYDNIPDTTTVII 135
Cdd:COG1376    77 GGYGiH-------GTPWPSS-IGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 15-135 1.05e-14

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: 64.68  E-value: 1.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  15 DYLIVTDLRNKYTYIFKKDNGgwgQLYKWQCTIGKPETPTITGIFYIsgrkpsfgtdeysvkyatrikggYYYHSVLYDS 94
Cdd:pfam03734   1 DRYIVVDLSEQRLLYLYENGG---LVLRYPVSVGRGDGPTPTGTFRI-----------------------IYIHDTGTPD 54

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1081285178  95 tgsyiiDGRLGEALSHGCIRLSTENAKWIYDNIPDTTTVII 135
Cdd:pfam03734  55 ------LFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 17-136 2.41e-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: 2.41e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  17 LIVTDLRNKYTYIFKKDNggwgQLYKWQCTIGKPETPTITGIFYISGRKPSFGTDEYSVKYATRIKGGYYYHSVLYDSTG 96
Cdd:cd16913     1 YIVVDLSEQRLYLYENGK----LVKTYPVSTGKPGTPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPLGPYALRLSGPGS 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1081285178  97 SYII-----DGRLGEALSHGCIRLSTENAKWIYDNIPDTTTVIIH 136
Cdd:cd16913    77 GIGIhgtpwPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
18-135 8.85e-16

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 68.35  E-value: 8.85e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  18 IVTDLRNKYTYIFKKDnggwGQLYKWQCTIGKPETPTITGIFYISGRKP---SFGTDEYSV-----------KYATRIKG 83
Cdd:COG1376     1 IVVDLSEQRLYVYEDG----GLVRTYPVSVGRPGFPTPTGTFRVLRKAEnptWTPPAEMPAgmpggpdnplgPYALYLSD 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1081285178  84 GYYY-HsvlydstGSYIIDGrLGEALSHGCIRLSTENAKWIYDNIPDTTTVII 135
Cdd:COG1376    77 GGYGiH-------GTPWPSS-IGRNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 15-135 1.05e-14

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: 64.68  E-value: 1.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1081285178  15 DYLIVTDLRNKYTYIFKKDNGgwgQLYKWQCTIGKPETPTITGIFYIsgrkpsfgtdeysvkyatrikggYYYHSVLYDS 94
Cdd:pfam03734   1 DRYIVVDLSEQRLLYLYENGG---LVLRYPVSVGRGDGPTPTGTFRI-----------------------IYIHDTGTPD 54

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1081285178  95 tgsyiiDGRLGEALSHGCIRLSTENAKWIYDNIPDTTTVII 135
Cdd:pfam03734  55 ------LFGLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 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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