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Conserved domains on  [gi|16802859|ref|NP_464344|]
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PhnB protein [Listeria monocytogenes EGD-e]

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 ...
 5-132 4.31e-43

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: 138.17  E-value: 4.31e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEMNNfDGDAVFGERLMHSRLAKNGEEFIYITDAPYDGFTIGNRVTIL 83
Cdd:cd06588   2 TPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP-DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAISLS 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 16802859  84 INFETEDDIKYAYEVLSATGKVEMELQVAFWGSTYAQVTDRFGVFWQLN 132
Cdd:cd06588  81 VDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 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 ...
 5-132 4.31e-43

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: 138.17  E-value: 4.31e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEMNNfDGDAVFGERLMHSRLAKNGEEFIYITDAPYDGFTIGNRVTIL 83
Cdd:cd06588   2 TPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP-DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAISLS 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 16802859  84 INFETEDDIKYAYEVLSATGKVEMELQVAFWGSTYAQVTDRFGVFWQLN 132
Cdd:cd06588  81 VDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-132 1.95e-20

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 80.28  E-value: 1.95e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   4 AVPYLVFNGeGQDALTFYADVFQAKITSVQRfkemnnfDGDavfgERLMHSRLAKNGEEfIYITDAPYDG-FTIGNRVTI 82
Cdd:COG2764   2 VTPYLVVDD-AEEALEFYEDVFGFEVVFRMT-------DPD----GKIMHAELRIGGSV-LMLSDAPPDSpAAEGNGVSL 68

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 16802859  83 LINFeteDDIKYAYEVLSATG-KVEMELQVAFWGSTYAQVTDRFGVFWQLN 132
Cdd:COG2764  69 SLYV---DDVDALFARLVAAGaTVVMPLQDTFWGDRFGMVRDPFGVLWMIN 116
PRK10148 PRK10148
VOC family metalloprotein YjdN;
6-136 4.39e-12

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 59.53  E-value: 4.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859    6 PYLVFNGEGQDALTFYADVFQAKITSVQRFKEMNNFDGDAVFG---------ERLMHSRLAKNGEEfIYITD------AP 70
Cdd:PRK10148   5 PYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAQDSEEGcpsgmqfpdTAIAHANVRIAGSD-IMMSDaipsgkAH 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16802859   71 YDGFTIgnrvtILinfETED--DIKYAYEVLSATGKVEMELQVAFWGSTYAQVTDRFGVFWQLNFDKK 136
Cdd:PRK10148  84 YSGFTL-----VL---DTQDveEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMINVVKQ 143
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 5-131 4.10e-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: 56.16  E-value: 4.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859     5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEmnNFDGDAvfgERLMHSRLAKNGEEFIYITDAPYDGFTIGnrVTIL 83
Cdd:pfam06983   4 TPCLWFDGQAEEAAEFYVSLFpNSEIGSVNRYPE--DGPGKP---GSVLTVEFTLNGQPFIALNGGPNFKFNEA--VSFQ 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 16802859    84 INFETEDDIKYAYEVLSATGKVEmelqvafwgSTYAQVTDRFGVFWQL 131
Cdd:pfam06983  77 VTCKDQEEVDRYWNALSENGGPE---------SQCGWLKDKFGVSWQI 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 ...
 5-132 4.31e-43

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: 138.17  E-value: 4.31e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEMNNfDGDAVFGERLMHSRLAKNGEEFIYITDAPYDGFTIGNRVTIL 83
Cdd:cd06588   2 TPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP-DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAISLS 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 16802859  84 INFETEDDIKYAYEVLSATGKVEMELQVAFWGSTYAQVTDRFGVFWQLN 132
Cdd:cd06588  81 VDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-132 1.95e-20

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 80.28  E-value: 1.95e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   4 AVPYLVFNGeGQDALTFYADVFQAKITSVQRfkemnnfDGDavfgERLMHSRLAKNGEEfIYITDAPYDG-FTIGNRVTI 82
Cdd:COG2764   2 VTPYLVVDD-AEEALEFYEDVFGFEVVFRMT-------DPD----GKIMHAELRIGGSV-LMLSDAPPDSpAAEGNGVSL 68

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 16802859  83 LINFeteDDIKYAYEVLSATG-KVEMELQVAFWGSTYAQVTDRFGVFWQLN 132
Cdd:COG2764  69 SLYV---DDVDALFARLVAAGaTVVMPLQDTFWGDRFGMVRDPFGVLWMIN 116
PRK10148 PRK10148
VOC family metalloprotein YjdN;
6-136 4.39e-12

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 59.53  E-value: 4.39e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859    6 PYLVFNGEGQDALTFYADVFQAKITSVQRFKEMNNFDGDAVFG---------ERLMHSRLAKNGEEfIYITD------AP 70
Cdd:PRK10148   5 PYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAQDSEEGcpsgmqfpdTAIAHANVRIAGSD-IMMSDaipsgkAH 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 16802859   71 YDGFTIgnrvtILinfETED--DIKYAYEVLSATGKVEMELQVAFWGSTYAQVTDRFGVFWQLNFDKK 136
Cdd:PRK10148  84 YSGFTL-----VL---DTQDveEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMINVVKQ 143
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 5-131 4.10e-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: 56.16  E-value: 4.10e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859     5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEmnNFDGDAvfgERLMHSRLAKNGEEFIYITDAPYDGFTIGnrVTIL 83
Cdd:pfam06983   4 TPCLWFDGQAEEAAEFYVSLFpNSEIGSVNRYPE--DGPGKP---GSVLTVEFTLNGQPFIALNGGPNFKFNEA--VSFQ 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 16802859    84 INFETEDDIKYAYEVLSATGKVEmelqvafwgSTYAQVTDRFGVFWQL 131
Cdd:pfam06983  77 VTCKDQEEVDRYWNALSENGGPE---------SQCGWLKDKFGVSWQI 115
COG3865 COG3865
Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General ...
 5-131 2.34e-10

Glyoxalase superfamily enzyme, possible 3-demethylubiquinone-9 3-methyltransferase [General function prediction only];


Pssm-ID: 443074  Cd Length: 156  Bit Score: 54.77  E-value: 2.34e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   5 VPYLVFNGEGQDALTFYADVF-QAKITSVQRFKEMNNF--DGDAVFGE-RLMhsrlaknGEEFIYITDAPYDGFTigNRV 80
Cdd:COG3865   5 TPCLWFDGQAEEAAEFYVSVFpDSRITAVTRYPEDGPGgpAGSVLTVEfTLA-------GQPFMALNGGPLFKFN--EAV 75

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 16802859  81 TILINFETEDDIKYAYEVLSATGKVEMelqvafwgstYAQVTDRFGVFWQL 131
Cdd:COG3865  76 SFQVNCEDQAEVDRLWDALSAGGEESQ----------CGWLKDRFGLSWQI 116
VOC_like cd07246
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 6-131 6.32e-09

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: 50.37  E-value: 6.32e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859   6 PYLVFNGEGqDALTFYADVFQAKitsvqrfkEMNNFDGDavfGERLMHSRLAKNGEEFiYITDA-PYDGF---TIGNRVT 81
Cdd:cd07246   5 PYLVVEDAA-AAIAFYKKAFGAE--------ELGRTTQE---DGRVGHAELRIGGTVV-MVADEnPERGAlspTKLGGTP 71

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 16802859  82 ILINFETEDdIKYAYEV-LSATGKVEMELQVAFWGSTYAQVTDRFGVFWQL 131
Cdd:cd07246  72 VIFHLYVED-VDATFARaVAAGAVVVEPVEDQFWGDRVGKVKDPFGHVWWL 121
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
7-131 3.92e-07

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 45.90  E-value: 3.92e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16802859     7 YLVFNGEGQDALTFYADVFQAKITSVQRFKEMNNFDGDAVFGERLMHSrLAKNGeefiyiTDAPYDGFTIGNrvTILINF 86
Cdd:pfam00903   5 VALRVGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFLAGGRVLE-LLLNE------TPPPAAAGFGGH--HIAFIA 75

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 16802859    87 ETEDDIKYAYEVLSATG-KVEMELQVAFWGSTYAQVTDRFGVFWQL 131
Cdd:pfam00903  76 FSVDDVDAAYDRLKAAGvEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
 
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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