NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1710412040|gb|QDR81224|]
View 

L,D-transpeptidase catalytic domain [Sporomusa termitida]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
5-110 5.27e-32

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


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 108.79  E-value: 5.27e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEK-----------LIFDKPGEFD--LGSRRLVLSSDKTC 71
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKaenptwtppaeMPAGMPGGPDnpLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1710412040  72 LHGS-WDGPVEGYVSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:COG1376    81 IHGTpWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
5-110 5.27e-32

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 108.79  E-value: 5.27e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEK-----------LIFDKPGEFD--LGSRRLVLSSDKTC 71
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKaenptwtppaeMPAGMPGGPDnpLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1710412040  72 LHGS-WDGPVEGYVSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:COG1376    81 IHGTpWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 5-110 2.87e-30

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: 104.31  E-value: 2.87e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEKLI--------FDKPGEFD-LGSRRLVLSSDKTC--LH 73
Cdd:cd16913     2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKnptwtgppSIPPGPYNpLGPYALRLSGPGSGigIH 81

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1710412040  74 GS-WDGPVEGYVSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:cd16913    82 GTpWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVV 119
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 5-111 7.32e-22

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: 82.01  E-value: 7.32e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHR-AYYYEDNQLIREYPVGSGKAETPTPPGSYEVIeklifdkpgefdlgsrrlvlssdktCLHGS---WDGPV 80
Cdd:pfam03734   4 IVVDLSEQRlLYLYENGGLVLRYPVSVGRGDGPTPTGTFRII-------------------------YIHDTgtpDLFGL 58

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1710412040  81 EGYVSGGCVRMYNKDIEELFEKMEIGAPVVM 111
Cdd:pfam03734  59 GRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PRK06132 PRK06132
hypothetical protein; Provisional
 5-110 9.67e-09

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 51.21  E-value: 9.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEKlifDKPGEFDLGS-------RRLVLSSdkTCLHGswd 77
Cdd:PRK06132   63 IVVSLDEQRLYVYDNGILIAVSTVSTGKRGHETPTGVFSILQK---DKDHRSNIYSnapmpymQRLTWSG--IALHA--- 134

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1710412040  78 GPVEGY-VSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:PRK06132  135 GNLPGYpASHGCVRLPSAFAKKLYGWTRMGTTVI 168
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
5-110 5.27e-32

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 108.79  E-value: 5.27e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEK-----------LIFDKPGEFD--LGSRRLVLSSDKTC 71
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPGFPTPTGTFRVLRKaenptwtppaeMPAGMPGGPDnpLGPYALYLSDGGYG 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1710412040  72 LHGS-WDGPVEGYVSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:COG1376    81 IHGTpWPSSIGRNVSHGCIRLSNEDAKWLYDRVPVGTPVV 120
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 5-110 2.87e-30

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: 104.31  E-value: 2.87e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEKLI--------FDKPGEFD-LGSRRLVLSSDKTC--LH 73
Cdd:cd16913     2 IVVDLSEQRLYLYENGKLVKTYPVSTGKPGTPTPTGTFRITRKVKnptwtgppSIPPGPYNpLGPYALRLSGPGSGigIH 81

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1710412040  74 GS-WDGPVEGYVSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:cd16913    82 GTpWPSSIGRPASHGCIRLSNEDAKELYDWVPVGTPVV 119
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 5-111 7.32e-22

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: 82.01  E-value: 7.32e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHR-AYYYEDNQLIREYPVGSGKAETPTPPGSYEVIeklifdkpgefdlgsrrlvlssdktCLHGS---WDGPV 80
Cdd:pfam03734   4 IVVDLSEQRlLYLYENGGLVLRYPVSVGRGDGPTPTGTFRII-------------------------YIHDTgtpDLFGL 58

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1710412040  81 EGYVSGGCVRMYNKDIEELFEKMEIGAPVVM 111
Cdd:pfam03734  59 GRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PRK06132 PRK06132
hypothetical protein; Provisional
 5-110 9.67e-09

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 51.21  E-value: 9.67e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   5 VIVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEKlifDKPGEFDLGS-------RRLVLSSdkTCLHGswd 77
Cdd:PRK06132   63 IVVSLDEQRLYVYDNGILIAVSTVSTGKRGHETPTGVFSILQK---DKDHRSNIYSnapmpymQRLTWSG--IALHA--- 134

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1710412040  78 GPVEGY-VSGGCVRMYNKDIEELFEKMEIGAPVV 110
Cdd:PRK06132  135 GNLPGYpASHGCVRLPSAFAKKLYGWTRMGTTVI 168
PRK12472 PRK12472
hypothetical protein; Provisional
 6-111 3.04e-08

hypothetical protein; Provisional


Pssm-ID: 237110 [Multi-domain]  Cd Length: 508  Bit Score: 49.87  E-value: 3.04e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710412040   6 IVNLTTHRAYYYEDNQLIREYPVGSGKAETPTPPGSYEVIEKLIFDKPGEFDLGS----RRLVLSSdkTCLHGswdGPVE 81
Cdd:PRK12472   57 IVSIKSQRVTLYDADGWILRAPVSTGTTGRETPAGVFAIVEKDKDHHSTMYDDAWmpnmQRITWNG--IALHG---GPLP 131

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1710412040  82 GY-VSGGCVRMYNKDIEELFEKMEIGAPVVM 111
Cdd:PRK12472  132 GYaASHGCVRMPYGFAEKLFDKTRIGMRVIV 162
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH