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Conserved domains on  [gi|1184710545|ref|WP_085269654|]
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L,D-transpeptidase family protein [Mycobacterium parmense]

Protein Classification

L,D-transpeptidase( domain architecture ID 11599005)

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

CATH:  2.40.440.10|2.60.40.3710
EC:  2.3.2.-
Gene Ontology:  GO:0018104|GO:0071972
PubMed:  18266857
SCOP:  4002015

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
127-266 3.63e-33

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


:

Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 117.27  E-value: 3.63e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 127 VASISDHTFTVSIDGVEAGptppvptphhrphfgeqgVLPASMGRPEFPTPVGTYTVLSKERSLIMDSSSVGiPVDDPDG 206
Cdd:COG1376     2 VVDLSEQRLYVYEDGGLVR------------------TYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEM-PAGMPGG 62

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1184710545 207 YRLPV-DYAVRITNHGLFVHSAPWaVNSLGlENVSHGCISLSPQDAEWYYNAVHVGDPVIV 266
Cdd:COG1376    63 PDNPLgPYALYLSDGGYGIHGTPW-PSSIG-RNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
LDT_IgD_like_1 cd13431
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 30-123 2.83e-29

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the first (N-terminal) repeat in LdtMt2 and related proteins.


:

Pssm-ID: 240446  Cd Length: 95  Bit Score: 106.24  E-value: 2.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  30 ASRPSGPPIASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMAL 109
Cdd:cd13431     2 PAPPLPVPVATVSPADGAVVGVAHPVVVTFADPVADRAAAENAIGITVAGPVAGGFSWTDDEPLGWTPTYFWPAHATVTV 81

                          90
                  ....*....|....
gi 1184710545 110 SVGGVATEFETGPA 123
Cdd:cd13431    82 GAGGTRTSFRTGDA 95
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
127-266 3.63e-33

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 117.27  E-value: 3.63e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 127 VASISDHTFTVSIDGVEAGptppvptphhrphfgeqgVLPASMGRPEFPTPVGTYTVLSKERSLIMDSSSVGiPVDDPDG 206
Cdd:COG1376     2 VVDLSEQRLYVYEDGGLVR------------------TYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEM-PAGMPGG 62

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1184710545 207 YRLPV-DYAVRITNHGLFVHSAPWaVNSLGlENVSHGCISLSPQDAEWYYNAVHVGDPVIV 266
Cdd:COG1376    63 PDNPLgPYALYLSDGGYGIHGTPW-PSSIG-RNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
LDT_IgD_like_1 cd13431
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 30-123 2.83e-29

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the first (N-terminal) repeat in LdtMt2 and related proteins.


Pssm-ID: 240446  Cd Length: 95  Bit Score: 106.24  E-value: 2.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  30 ASRPSGPPIASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMAL 109
Cdd:cd13431     2 PAPPLPVPVATVSPADGAVVGVAHPVVVTFADPVADRAAAENAIGITVAGPVAGGFSWTDDEPLGWTPTYFWPAHATVTV 81

                          90
                  ....*....|....
gi 1184710545 110 SVGGVATEFETGPA 123
Cdd:cd13431    82 GAGGTRTSFRTGDA 95
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 166-267 2.31e-24

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: 94.30  E-value: 2.31e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 166 PASMGRPEFPTPVGTYTVLSKERslimDSSSVGIPVDDPDGYRLPVDYAVRITN--HGLFVHSAPWavNSLGLENVSHGC 243
Cdd:cd16913    24 PVSTGKPGTPTPTGTFRITRKVK----NPTWTGPPSIPPGPYNPLGPYALRLSGpgSGIGIHGTPW--PSSIGRPASHGC 97

                          90       100
                  ....*....|....*....|....
gi 1184710545 244 ISLSPQDAEWYYNAVHVGDPVIVQ 267
Cdd:cd16913    98 IRLSNEDAKELYDWVPVGTPVVIY 121
Big_10 pfam17964
Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with ...
 32-137 3.33e-18

Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.


Pssm-ID: 465591 [Multi-domain]  Cd Length: 182  Bit Score: 79.59  E-value: 3.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  32 RPSGPPIASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMALSV 111
Cdd:pfam17964  79 SPANTTSGTLTPLDGSTVGVGMPISINFDKPVTDKAAVEKAITVTTSPAVEGAWHWFGDQRVDWRPKEYWPPGTKVTVDA 158

                          90       100
                  ....*....|....*....|....*...
gi 1184710545 112 G--GVatefETGPAVVGVASiSDHTFTV 137
Cdd:pfam17964 159 RlyGV----DLGDGVYGQQD-RTVTFTI 181
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 166-266 4.26e-12

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: 60.83  E-value: 4.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 166 PASMGRPEFPTPVGTYTVLskerslimdsssvgipvddpdgyrlpvdyavritnhglFVHSAPWAVNSLGLENVSHGCIS 245
Cdd:pfam03734  27 PVSVGRGDGPTPTGTFRII--------------------------------------YIHDTGTPDLFGLGRRRSHGCIR 68

                          90       100
                  ....*....|....*....|.
gi 1184710545 246 LSPQDAEWYYNAVHVGDPVIV 266
Cdd:pfam03734  69 LSNEDAKELYDRVLVGTPVVI 89
 
Name Accession Description Interval E-value
ErfK COG1376
Lipoprotein-anchoring transpeptidase ErfK/SrfK [Cell wall/membrane/envelope biogenesis];
127-266 3.63e-33

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


Pssm-ID: 440986 [Multi-domain]  Cd Length: 121  Bit Score: 117.27  E-value: 3.63e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 127 VASISDHTFTVSIDGVEAGptppvptphhrphfgeqgVLPASMGRPEFPTPVGTYTVLSKERSLIMDSSSVGiPVDDPDG 206
Cdd:COG1376     2 VVDLSEQRLYVYEDGGLVR------------------TYPVSVGRPGFPTPTGTFRVLRKAENPTWTPPAEM-PAGMPGG 62

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1184710545 207 YRLPV-DYAVRITNHGLFVHSAPWaVNSLGlENVSHGCISLSPQDAEWYYNAVHVGDPVIV 266
Cdd:COG1376    63 PDNPLgPYALYLSDGGYGIHGTPW-PSSIG-RNVSHGCIRLSNEDAKWLYDRVPVGTPVVV 121
LDT_IgD_like_1 cd13431
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 30-123 2.83e-29

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the first (N-terminal) repeat in LdtMt2 and related proteins.


Pssm-ID: 240446  Cd Length: 95  Bit Score: 106.24  E-value: 2.83e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  30 ASRPSGPPIASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMAL 109
Cdd:cd13431     2 PAPPLPVPVATVSPADGAVVGVAHPVVVTFADPVADRAAAENAIGITVAGPVAGGFSWTDDEPLGWTPTYFWPAHATVTV 81

                          90
                  ....*....|....
gi 1184710545 110 SVGGVATEFETGPA 123
Cdd:cd13431    82 GAGGTRTSFRTGDA 95
YkuD_like cd16913
L,D-transpeptidases/carboxypeptidases similar to Bacillus YkuD; Members of the YkuD-like ...
 166-267 2.31e-24

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: 94.30  E-value: 2.31e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 166 PASMGRPEFPTPVGTYTVLSKERslimDSSSVGIPVDDPDGYRLPVDYAVRITN--HGLFVHSAPWavNSLGLENVSHGC 243
Cdd:cd16913    24 PVSTGKPGTPTPTGTFRITRKVK----NPTWTGPPSIPPGPYNPLGPYALRLSGpgSGIGIHGTPW--PSSIGRPASHGC 97

                          90       100
                  ....*....|....*....|....
gi 1184710545 244 ISLSPQDAEWYYNAVHVGDPVIVQ 267
Cdd:cd16913    98 IRLSNEDAKELYDWVPVGTPVVIY 121
LDT_IgD_like_2 cd13432
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 39-137 3.82e-21

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain; this model represents the repeat adjacent to the catalytic domain.


Pssm-ID: 240447  Cd Length: 99  Bit Score: 85.26  E-value: 3.82e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  39 ASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMALSVG--GVat 116
Cdd:cd13432     3 ASVNPLDGETVGVGMPVIVTFDEPVTDRAAVEKALKVTTSPPVEGAWYWLSDREVHWRPKEYWPPGTKVTVDANlyGV-- 80

                          90       100
                  ....*....|....*....|.
gi 1184710545 117 efETGPAVVGVASISdHTFTV 137
Cdd:cd13432    81 --DLGDGVYGQEDRS-TTFTI 98
Big_10 pfam17964
Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with ...
 32-137 3.33e-18

Bacterial Ig domain; This entry represents a bacterial Ig-like domain found associated with transpeptidase domains.


Pssm-ID: 465591 [Multi-domain]  Cd Length: 182  Bit Score: 79.59  E-value: 3.33e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  32 RPSGPPIASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDVVQWVPDRFWPAHSTMALSV 111
Cdd:pfam17964  79 SPANTTSGTLTPLDGSTVGVGMPISINFDKPVTDKAAVEKAITVTTSPAVEGAWHWFGDQRVDWRPKEYWPPGTKVTVDA 158

                          90       100
                  ....*....|....*....|....*...
gi 1184710545 112 G--GVatefETGPAVVGVASiSDHTFTV 137
Cdd:pfam17964 159 RlyGV----DLGDGVYGQQD-RTVTFTI 181
LDT_IgD_like cd13430
IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found ...
 39-133 2.92e-12

IgD-like repeat domain of mycobacterial L,D-transpeptidases; Immunoglobulin-like domain found in actinobacterial L,D-transpeptidases, including Mycobacterium tuberculosis LdtMt2, which is a non-classical transpeptidase that generates 3->3 transpeptide linkages. LdtMt2 is associated with virulence and resistance to amoxicillin. This domain may occur in a tandem-repeat arrangement and is found N-terminal to the catalytic L,D-transpeptidase domain.


Pssm-ID: 240445  Cd Length: 98  Bit Score: 61.58  E-value: 2.92e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545  39 ASVLPARGAVVGVAHPIVVRFRVPIADRHAAERALDVRSAPAMTGRFEWLDNDV-VQWVPDRFWPAHSTMALSVGGVATE 117
Cdd:cd13430     2 PYVMPGDGEVVGVGAPVAIRFDENIADRGAAEKAITITTDPPVEGAFYWLPDGRrVRWRPEHFWKPGTAVDVAANTYGLD 81

                          90
                  ....*....|....*.
gi 1184710545 118 FetGPAVVGVASISDH 133
Cdd:cd13430    82 L--GEGMFGADNVQLH 95
YkuD pfam03734
L,D-transpeptidase catalytic domain; This family of proteins are found in a range of bacteria. ...
 166-266 4.26e-12

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: 60.83  E-value: 4.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1184710545 166 PASMGRPEFPTPVGTYTVLskerslimdsssvgipvddpdgyrlpvdyavritnhglFVHSAPWAVNSLGLENVSHGCIS 245
Cdd:pfam03734  27 PVSVGRGDGPTPTGTFRII--------------------------------------YIHDTGTPDLFGLGRRRSHGCIR 68

                          90       100
                  ....*....|....*....|.
gi 1184710545 246 LSPQDAEWYYNAVHVGDPVIV 266
Cdd:pfam03734  69 LSNEDAKELYDRVLVGTPVVI 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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