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Conserved domains on  [gi|58176889|pdb|1U6L|B]
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Chain B, Crystal structure of protein PA1353 from Pseudomonas aeruginosa

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 ...
 5-134 9.82e-45

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: 142.80  E-value: 9.82e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B        5 IVPYLIFNGNCREAFSCYHQHL-GGTLEA*LPFGDSPEcgDIPADWKDKI*HARLVVGSFAL*ASDNHPAYPYEGIKGCS 83
Cdd:cd06588   1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP--DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAIS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
1U6L_B       84 ISLNVDSKAEAERLFNALAEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VN 134
Cdd:cd06588  79 LSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 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 ...
 5-134 9.82e-45

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: 142.80  E-value: 9.82e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B        5 IVPYLIFNGNCREAFSCYHQHL-GGTLEA*LPFGDSPEcgDIPADWKDKI*HARLVVGSFAL*ASDNHPAYPYEGIKGCS 83
Cdd:cd06588   1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP--DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAIS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
1U6L_B       84 ISLNVDSKAEAERLFNALAEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VN 134
Cdd:cd06588  79 LSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-136 8.92e-33

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 112.26  E-value: 8.92e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B        4 QIVPYLIFNgNCREAFSCYHQHLGGTLEA*LPFGDspecgdipadwkDKI*HARLVVGSFAL*ASDNHPAYPYEGIKGCS 83
Cdd:COG2764   1 SVTPYLVVD-DAEEALEFYEDVFGFEVVFRMTDPD------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNGVS 67

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
1U6L_B       84 ISLNVDskaEAERLFNAL-AEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VNCE 136
Cdd:COG2764  68 LSLYVD---DVDALFARLvAAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINTP 118
PRK10148 PRK10148
VOC family metalloprotein YjdN;
7-134 2.49e-21

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 83.80  E-value: 2.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B         7 PYLIFNGNCREAFSCYHQHLGGTLEA*LPFGDSPECGDIPADW--------KDKI*HARLVVGSFAL*ASDNHPAyPYEG 78
Cdd:PRK10148   5 PYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAQDSEEGcpsgmqfpDTAIAHANVRIAGSDIMMSDAIPS-GKAH 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
1U6L_B        79 IKGCSISLNVDSKAEAERLFNALAEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VN 134
Cdd:PRK10148  84 YSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMIN 139
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
4-133 2.35e-14

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 65.16  E-value: 2.35e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B          4 QIVPYLIFNGNCREAFSCYHQHLGGTLEA*lpfgdspecgDIPADWKDKI*HARLVVGSFAL*ASDNHPAYPYE-GIKGC 82
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVE-----------ETDAGEEGGLRSAFFLAGGRVLELLLNETPPPAAaGFGGH 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
1U6L_B         83 SISLNVDSKAEAERLFNALAE-GGSVQ*PLGPTFWAASFG*FTDRFGVAW*V 133
Cdd:pfam00903  70 HIAFIAFSVDDVDAAYDRLKAaGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
 
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 ...
 5-134 9.82e-45

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: 142.80  E-value: 9.82e-45
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B        5 IVPYLIFNGNCREAFSCYHQHL-GGTLEA*LPFGDSPEcgDIPADWKDKI*HARLVVGSFAL*ASDNHPAYPYEGIKGCS 83
Cdd:cd06588   1 ITPYLWFNGNAEEALEFYAEVFpGGEILSLTRYGEGPP--DFPEGDEGKVMHAEFTLGGQTLMASDDGPGFPFTFGNAIS 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
1U6L_B       84 ISLNVDSKAEAERLFNALAEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VN 134
Cdd:cd06588  79 LSVDCDSQEEADRLFEKLSEGGEVLMPLQETFWGARYGWVKDKFGVSWQIN 129
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
4-136 8.92e-33

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 112.26  E-value: 8.92e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B        4 QIVPYLIFNgNCREAFSCYHQHLGGTLEA*LPFGDspecgdipadwkDKI*HARLVVGSFAL*ASDNHPAYPYEGIKGCS 83
Cdd:COG2764   1 SVTPYLVVD-DAEEALEFYEDVFGFEVVFRMTDPD------------GKIMHAELRIGGSVLMLSDAPPDSPAAEGNGVS 67

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
1U6L_B       84 ISLNVDskaEAERLFNAL-AEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VNCE 136
Cdd:COG2764  68 LSLYVD---DVDALFARLvAAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINTP 118
PRK10148 PRK10148
VOC family metalloprotein YjdN;
7-134 2.49e-21

VOC family metalloprotein YjdN;


Pssm-ID: 236656  Cd Length: 147  Bit Score: 83.80  E-value: 2.49e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B         7 PYLIFNGNCREAFSCYHQHLGGTLEA*LPFGDSPECGDIPADW--------KDKI*HARLVVGSFAL*ASDNHPAyPYEG 78
Cdd:PRK10148   5 PYLSFAGNCADAIAYYQQTLGAELLYKISFGEMPKSAQDSEEGcpsgmqfpDTAIAHANVRIAGSDIMMSDAIPS-GKAH 83

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
1U6L_B        79 IKGCSISLNVDSKAEAERLFNALAEGGSVQ*PLGPTFWAASFG*FTDRFGVAW*VN 134
Cdd:PRK10148  84 YSGFTLVLDTQDVEEGKRWFDNLAANGKIEMAWQETFWAHGFGKVTDKFGVPWMIN 139
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
4-133 2.35e-14

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 65.16  E-value: 2.35e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B          4 QIVPYLIFNGNCREAFSCYHQHLGGTLEA*lpfgdspecgDIPADWKDKI*HARLVVGSFAL*ASDNHPAYPYE-GIKGC 82
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVE-----------ETDAGEEGGLRSAFFLAGGRVLELLLNETPPPAAaGFGGH 69

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
1U6L_B         83 SISLNVDSKAEAERLFNALAE-GGSVQ*PLGPTFWAASFG*FTDRFGVAW*V 133
Cdd:pfam00903  70 HIAFIAFSVDDVDAAYDRLKAaGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
3-dmu-9_3-mt pfam06983
3-demethylubiquinone-9 3-methyltransferase; This family represents a conserved region ...
 5-133 4.28e-06

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: 43.06  E-value: 4.28e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B          5 IVPYLIFNGNCREAFSCYhqhlggtleA*LpFGDSpECGDI---PADWKDK---I*HARLVVGSFAL*ASDNHPAYPY-E 77
Cdd:pfam06983   3 ITPCLWFDGQAEEAAEFY---------VSL-FPNS-EIGSVnryPEDGPGKpgsVLTVEFTLNGQPFIALNGGPNFKFnE 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
1U6L_B         78 GIkgcSISLNVDSKAEAERLFNALAEGGsvq*plGPtfwAASFG*FTDRFGVAW*V 133
Cdd:pfam06983  72 AV---SFQVTCKDQEEVDRYWNALSENG------GP---ESQCGWLKDKFGVSWQI 115
VOC_like cd07246
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 52-133 5.73e-04

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: 37.66  E-value: 5.73e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
1U6L_B       52 KI*HARLVVGSFAL*ASDNHPAY-----PYEGIKGCSISLNVDSkaeAERLFN-ALAEGGSVQ*PLGPTFWAASFG*FTD 125
Cdd:cd07246  37 RVGHAELRIGGTVVMVADENPERgalspTKLGGTPVIFHLYVED---VDATFArAVAAGAVVVEPVEDQFWGDRVGKVKD 113


                ....*...
1U6L_B      126 RFGVAW*V 133
Cdd:cd07246 114 PFGHVWWL 121
COG3607 COG3607
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 81-131 8.96e-03

Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function prediction only];


Pssm-ID: 442825  Cd Length: 126  Bit Score: 34.42  E-value: 8.96e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
1U6L_B       81 GCSISLNVDSKAEAERLFN-ALAEGGSVQ*PLGPTFWAASfG*FTD----RFGVAW 131
Cdd:COG3607  72 EVLLALNVESREEVDALVAkALAAGGTVLKPPQDVGGMYS-GYFADpdghLWEVAW 126
 
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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