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Conserved domains on  [gi|247544900|gb|ACT01919|]
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3-demethylubiquinone-9 3-methyltransferase [Paenibacillus sp. JDR-2]

Protein Classification

VOC family protein( domain architecture ID 10159541)

vicinal oxygen chelate (VOC) family protein uses a metal center to coordinate a substrate, intermediate, or transition state through vicinal oxygen atoms

CATH:  3.10.180.10
PubMed:  21820381

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 2.79e-39

Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases.


:

Pssm-ID: 319899  Cd Length: 129  Bit Score: 128.54  E-value: 2.79e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   5 LTPFIMLDGVAREAIAFYEQAL-DAKVVFKQTFGEAPGEAGqavsEQARDRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDFP----EGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 247544900  84 VNICVTVVDKEQARKYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIF 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
 
Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 2.79e-39

Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases.


Pssm-ID: 319899  Cd Length: 129  Bit Score: 128.54  E-value: 2.79e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   5 LTPFIMLDGVAREAIAFYEQAL-DAKVVFKQTFGEAPGEAGqavsEQARDRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDFP----EGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 247544900  84 VNICVTVVDKEQARKYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIF 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-137 9.17e-26

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 93.77  E-value: 9.17e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   4 QLTPFIMLDGvAREAIAFYEQALDAKVVFKQTFGEapgeagqavseqarDRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ 83
Cdd:COG2764    1 SVTPYLVVDD-AEEALEFYEDVFGFEVVFRMTDPD--------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNG 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 247544900  84 VNICVTVvdkEQARKYYEALK-EGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIFT 137
Cdd:COG2764   66 VSLSLYV---DDVDALFARLVaAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
PRK10148 PRK10148
VOC family metalloprotein YjdN;
5-135 8.45e-21

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 82.26  E-value: 8.45e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   5 LTPFIMLDGVAREAIAFYEQALDAKVVFKQTFGEAPGEA---------GQAVSEQArdrLAHSVLKIGGTDLFVADTNPE 75
Cdd:PRK10148   3 LSPYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAqdseegcpsGMQFPDTA---IAHANVRIAGSDIMMSDAIPS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900  76 VRfAQGKQVNICVTVVDKEQARKYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQI 135
Cdd:PRK10148  80 GK-AHYSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMI 138
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 5-135 1.09e-11

3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins.


Pssm-ID: 399756  Cd Length: 116  Bit Score: 57.70  E-value: 1.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900    5 LTPFIMLDGVAREAIAFYEQAL-DAKVVFKQTFGE-APGEAGQAVseqardrlaHSVLKIGGTDLFVADTNPEVRFAQGk 82
Cdd:pfam06983   3 ITPCLWFDGQAEEAAEFYVSLFpNSEIGSVNRYPEdGPGKPGSVL---------TVEFTLNGQPFIALNGGPNFKFNEA- 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 247544900   83 qVNICVTVVDKEQARKYYEALKEGGQvvlplqeiHFSpAYGMVTDKFGVTFQI 135
Cdd:pfam06983  73 -VSFQVTCKDQEEVDRYWNALSENGG--------PES-QCGWLKDKFGVSWQI 115
 
Name Accession Description Interval E-value
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 5-136 2.79e-39

Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to bleomycin resistance proteins, glyoxalase I, and type I extradiol dioxygenases.


Pssm-ID: 319899  Cd Length: 129  Bit Score: 128.54  E-value: 2.79e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   5 LTPFIMLDGVAREAIAFYEQAL-DAKVVFKQTFGEAPGEAGqavsEQARDRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ 83
Cdd:cd06588    1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPPDFP----EGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 247544900  84 VNICVTVVDKEQARKYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIF 136
Cdd:cd06588   77 ISLSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-137 9.17e-26

Zn-dependent glyoxalase, PhnB family [Energy production and conversion];


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 93.77  E-value: 9.17e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   4 QLTPFIMLDGvAREAIAFYEQALDAKVVFKQTFGEapgeagqavseqarDRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ 83
Cdd:COG2764    1 SVTPYLVVDD-AEEALEFYEDVFGFEVVFRMTDPD--------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNG 65

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 247544900  84 VNICVTVvdkEQARKYYEALK-EGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIFT 137
Cdd:COG2764   66 VSLSLYV---DDVDALFARLVaAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINT 117
PRK10148 PRK10148
VOC family metalloprotein YjdN;
5-135 8.45e-21

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 82.26  E-value: 8.45e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   5 LTPFIMLDGVAREAIAFYEQALDAKVVFKQTFGEAPGEA---------GQAVSEQArdrLAHSVLKIGGTDLFVADTNPE 75
Cdd:PRK10148   3 LSPYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAqdseegcpsGMQFPDTA---IAHANVRIAGSDIMMSDAIPS 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900  76 VRfAQGKQVNICVTVVDKEQARKYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQI 135
Cdd:PRK10148  80 GK-AHYSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMI 138
VOC_like cd07246
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 15-138 1.37e-13

uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping


Pssm-ID: 319910 [Multi-domain]  Cd Length: 124  Bit Score: 62.70  E-value: 1.37e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900  15 AREAIAFYEQALDAKVVFKQTfgeapGEAGqavseqardRLAHSVLKIGGTDLFVADTNPEVRFAQGKQ-----VNICVT 89
Cdd:cd07246   12 AAAAIAFYKKAFGAEELGRTT-----QEDG---------RVGHAELRIGGTVVMVADENPERGALSPTKlggtpVIFHLY 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 247544900  90 VVDKEQArkYYEALKEGGQVVLPLQEIHFSPAYGMVTDKFGVTFQIFTK 138
Cdd:cd07246   78 VEDVDAT--FARAVAAGAVVVEPVEDQFWGDRVGKVKDPFGHVWWLATP 124
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 5-135 1.09e-11

3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region approximately 100 residues long within a number of bacterial and archaeal 3-demethylubiquinone-9 3-methyltransferases (EC:2.1.1.64). Note that some family members contain more than one copy of this region, and that many members are hypothetical proteins.


Pssm-ID: 399756  Cd Length: 116  Bit Score: 57.70  E-value: 1.09e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900    5 LTPFIMLDGVAREAIAFYEQAL-DAKVVFKQTFGE-APGEAGQAVseqardrlaHSVLKIGGTDLFVADTNPEVRFAQGk 82
Cdd:pfam06983   3 ITPCLWFDGQAEEAAEFYVSLFpNSEIGSVNRYPEdGPGKPGSVL---------TVEFTLNGQPFIALNGGPNFKFNEA- 72

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 247544900   83 qVNICVTVVDKEQARKYYEALKEGGQvvlplqeiHFSpAYGMVTDKFGVTFQI 135
Cdd:pfam06983  73 -VSFQVTCKDQEEVDRYWNALSENGG--------PES-QCGWLKDKFGVSWQI 115
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
15-135 2.03e-05

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 41.28  E-value: 2.03e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900   15 AREAIAFYEQALDAKVVFKQTFGEAPGeagqavseqardrLAHSVLKIGGTDL-FVADTNPEVRFAQGKQVNICVTVVDK 93
Cdd:pfam00903  12 LEKSLDFYTDVLGFKLVEETDAGEEGG-------------LRSAFFLAGGRVLeLLLNETPPPAAAGFGGHHIAFIAFSV 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 247544900   94 EQARKYYEALKE-GGQVVLPLQEIHFSPAYGMVTDKFGVTFQI 135
Cdd:pfam00903  79 DDVDAAYDRLKAaGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
VOC_ShValD_like cd16361
vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein; ...
 17-137 8.46e-05

vicinal oxygen chelate (VOC) family protein similar to Streptomyces hygroscopicus ValD protein; This subfamily of vicinal oxygen chelate (VOC) family protein includes Streptomyces hygroscopicus ValD protein and similar proteins. ValD protein functions in validamycin biosynthetic pathway. The vicinal oxygen chelate (VOC) superfamily is composed of structurally related proteins with paired beta.alpha.beta.beta.beta motifs that provide a metal coordination environment with two or three open or readily accessible coordination sites to promote direct electrophilic participation of the metal ion in catalysis. VOC domain is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.


Pssm-ID: 319968  Cd Length: 150  Bit Score: 40.01  E-value: 8.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 247544900  17 EAIAFYEQALDAKVVFKQTFGEAPGEAGQ----AVSEQARDRLAHSVLKIG---GTDLF----VADTNPEVRFAQGKQVN 85
Cdd:cd16361   14 AAVEFYTDVLGAEVVYRSTPLAEGDRGGGemraAGFVPGFARARIAMLRLGpgpGIELFeykgPEQRAPVPRNSDVGIFH 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 247544900  86 ICVTVVDKEQARKYYEAlkEGGQVVLPLQEIHFSPA---YGMV--TDKFGVTFQIFT 137
Cdd:cd16361   94 FALQVDDVEAAAERLAA--AGGKVLMGPREIPDGGPgkgNRMVylRDPWGTLIELVS 148
 
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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