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Conserved domains on  [gi|1655122633|ref|WP_137607801|]
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L,D-transpeptidase/peptidoglycan binding protein [Lactiplantibacillus daoliensis]

Protein Classification

L,D-transpeptidase family protein( domain architecture ID 13779769)

L,D-transpeptidase family protein similar to L,D-transpeptidase that catalyzes the formation of 3->3 peptidoglycan cross-links

CATH:  2.40.440.10|1.10.269.20
EC:  2.3.2.-
Gene Ontology:  GO:0018104|GO:0071972|GO:0042834
PubMed:  18266857
SCOP:  4002015|4000465

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 ...
 341-464 3.24e-31

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: 116.25  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 341 YIEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQRNSTLKGDNDDGSDYAQP-VAYWMPF--GDTGQG 417
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPG-TPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPlGPYALRLsgPGSGIG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1655122633 418 IHDSPWQKQYGgtwykTHGSHGCVNTPPTEVAKVYDAIPVGTPVVIF 464
Cdd:cd16913    80 IHGTPWPSSIG-----RPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
PG_binding_4 pfam12229
Putative peptidoglycan binding domain; This domain is found associated with the L, ...
 205-321 5.02e-12

Putative peptidoglycan binding domain; This domain is found associated with the L,D-transpeptidase domain pfam03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).


:

Pssm-ID: 403443  Cd Length: 117  Bit Score: 62.42  E-value: 5.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 205 TSTSQNLKTAKKrTQKYASEKATYNINGNKFQIPHDTI-LSWLKVDKAGKVSLDQVAVKTYVDQLNDKYHTYHTTRTFKs 283
Cdd:pfam12229   2 TVTLEELGLSYD-IEEAVDEAYTYGRKGNIFERLKEILaAWKKGVDIKLRVSLDKEKLQAYIDEIAKEIDREPKDASFK- 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1655122633 284 TQRGDVKIDGGLYGWTIKSADETKALSKDVLAGKDFNR 321
Cdd:pfam12229  80 LAGGTVTVIPERPGRKLDVDKLLEDIIAALLDGKRTID 117
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 341-464 3.24e-31

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: 116.25  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 341 YIEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQRNSTLKGDNDDGSDYAQP-VAYWMPF--GDTGQG 417
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPG-TPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPlGPYALRLsgPGSGIG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1655122633 418 IHDSPWQKQYGgtwykTHGSHGCVNTPPTEVAKVYDAIPVGTPVVIF 464
Cdd:cd16913    80 IHGTPWPSSIG-----RPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
342-463 7.86e-31

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 115.34  E-value: 7.86e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 342 IEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQRN----STLKGDNDDGSDYAQPV-AYWMPFGDTGQ 416
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPG-FPTPTGTFRVLRKAENptwtPPAEMPAGMPGGPDNPLgPYALYLSDGGY 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1655122633 417 GIHDSPWQKQYGgtwykTHGSHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:COG1376    80 GIHGTPWPSSIG-----RNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 339-463 2.84e-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: 65.06  E-value: 2.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 339 STYIEVDKQAQHM-WVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWskqrnstlkgdnddgsdyaqpvaywmpfgdtgqG 417
Cdd:pfam03734   1 DRYIVVDLSEQRLlYLYENGGLVLRYPVSVGRGD-GPTPTGTFRII---------------------------------Y 46

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1655122633 418 IHDSPWQKQYggtWYKTHGSHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:pfam03734  47 IHDTGTPDLF---GLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PG_binding_4 pfam12229
Putative peptidoglycan binding domain; This domain is found associated with the L, ...
 205-321 5.02e-12

Putative peptidoglycan binding domain; This domain is found associated with the L,D-transpeptidase domain pfam03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).


Pssm-ID: 403443  Cd Length: 117  Bit Score: 62.42  E-value: 5.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 205 TSTSQNLKTAKKrTQKYASEKATYNINGNKFQIPHDTI-LSWLKVDKAGKVSLDQVAVKTYVDQLNDKYHTYHTTRTFKs 283
Cdd:pfam12229   2 TVTLEELGLSYD-IEEAVDEAYTYGRKGNIFERLKEILaAWKKGVDIKLRVSLDKEKLQAYIDEIAKEIDREPKDASFK- 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1655122633 284 TQRGDVKIDGGLYGWTIKSADETKALSKDVLAGKDFNR 321
Cdd:pfam12229  80 LAGGTVTVIPERPGRKLDVDKLLEDIIAALLDGKRTID 117
PRK06132 PRK06132
hypothetical protein; Provisional
 342-463 7.09e-07

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 51.21  E-value: 7.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 342 IEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQR--NSTLkgdnddgsdY-AQPvaywMPFgdtGQGI 418
Cdd:PRK06132   63 IVVSLDEQRLYVYDNGILIAVSTVSTGKRG-HETPTGVFSILQKDKdhRSNI---------YsNAP----MPY---MQRL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1655122633 419 hdspwqkqyggTW--YKTHG--------SHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:PRK06132  126 -----------TWsgIALHAgnlpgypaSHGCVRLPSAFAKKLYGWTRMGTTVII 169
 
Name Accession Description Interval E-value
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 341-464 3.24e-31

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: 116.25  E-value: 3.24e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 341 YIEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQRNSTLKGDNDDGSDYAQP-VAYWMPF--GDTGQG 417
Cdd:cd16913     1 YIVVDLSEQRLYLYENGKLVKTYPVSTGKPG-TPTPTGTFRITRKVKNPTWTGPPSIPPGPYNPlGPYALRLsgPGSGIG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1655122633 418 IHDSPWQKQYGgtwykTHGSHGCVNTPPTEVAKVYDAIPVGTPVVIF 464
Cdd:cd16913    80 IHGTPWPSSIG-----RPASHGCIRLSNEDAKELYDWVPVGTPVVIY 121
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
342-463 7.86e-31

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 115.34  E-value: 7.86e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 342 IEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQRN----STLKGDNDDGSDYAQPV-AYWMPFGDTGQ 416
Cdd:COG1376     1 IVVDLSEQRLYVYEDGGLVRTYPVSVGRPG-FPTPTGTFRVLRKAENptwtPPAEMPAGMPGGPDNPLgPYALYLSDGGY 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1655122633 417 GIHDSPWQKQYGgtwykTHGSHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:COG1376    80 GIHGTPWPSSIG-----RNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 339-463 2.84e-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: 65.06  E-value: 2.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 339 STYIEVDKQAQHM-WVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWskqrnstlkgdnddgsdyaqpvaywmpfgdtgqG 417
Cdd:pfam03734   1 DRYIVVDLSEQRLlYLYENGGLVLRYPVSVGRGD-GPTPTGTFRII---------------------------------Y 46

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1655122633 418 IHDSPWQKQYggtWYKTHGSHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:pfam03734  47 IHDTGTPDLF---GLGRRRSHGCIRLSNEDAKELYDRVLVGTPVVI 89
PG_binding_4 pfam12229
Putative peptidoglycan binding domain; This domain is found associated with the L, ...
 205-321 5.02e-12

Putative peptidoglycan binding domain; This domain is found associated with the L,D-transpeptidase domain pfam03734. The structure of this domain has been solved and shows a mixed alpha-beta fold composed of nine beta strands and four alpha helices. This domain is usually found to be duplicated. Therefore, it seems likely that this domain acts to bind the two unlinked peptidoglycan chains and bring them into close association so they can be cross linked by the transpeptidase domain (Bateman A pers. observation).


Pssm-ID: 403443  Cd Length: 117  Bit Score: 62.42  E-value: 5.02e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 205 TSTSQNLKTAKKrTQKYASEKATYNINGNKFQIPHDTI-LSWLKVDKAGKVSLDQVAVKTYVDQLNDKYHTYHTTRTFKs 283
Cdd:pfam12229   2 TVTLEELGLSYD-IEEAVDEAYTYGRKGNIFERLKEILaAWKKGVDIKLRVSLDKEKLQAYIDEIAKEIDREPKDASFK- 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1655122633 284 TQRGDVKIDGGLYGWTIKSADETKALSKDVLAGKDFNR 321
Cdd:pfam12229  80 LAGGTVTVIPERPGRKLDVDKLLEDIIAALLDGKRTID 117
PRK06132 PRK06132
hypothetical protein; Provisional
 342-463 7.09e-07

hypothetical protein; Provisional


Pssm-ID: 235709 [Multi-domain]  Cd Length: 359  Bit Score: 51.21  E-value: 7.09e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1655122633 342 IEVDKQAQHMWVYVDGQVKVSTDVVTGKPGqHETTTGVWSVWSKQR--NSTLkgdnddgsdY-AQPvaywMPFgdtGQGI 418
Cdd:PRK06132   63 IVVSLDEQRLYVYDNGILIAVSTVSTGKRG-HETPTGVFSILQKDKdhRSNI---------YsNAP----MPY---MQRL 125

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1655122633 419 hdspwqkqyggTW--YKTHG--------SHGCVNTPPTEVAKVYDAIPVGTPVVI 463
Cdd:PRK06132  126 -----------TWsgIALHAgnlpgypaSHGCVRLPSAFAKKLYGWTRMGTTVII 169
 
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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