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Conserved domains on  [gi|446335583|ref|WP_000413438|]
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MULTISPECIES: VOC family protein [Staphylococcus]

Protein Classification

VOC family protein( domain architecture ID 50733)

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
Gene Ontology:  GO:0046872|GO:0003824
PubMed:  21820381|11076500

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
VOC super family cl14632
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 6-121 2.87e-29

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 is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. 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). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases.


The actual alignment was detected with superfamily member cd07263:

Pssm-ID: 472697 [Multi-domain]  Cd Length: 120  Bit Score: 102.38  E-value: 2.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   6 QVMLYVDDVEKAKAFWTETLEFVVVSETPLaEDYVAVEVSPTKDAETSLTIMAKEFIEK--YSPEVNLGTPSLMFKEKNF 83
Cdd:cd07263    1 QVMLYVDDQDKALDFYVEKLGFEVVEDVPM-GGMRWVTVAPPGSPGTSLLLEPKAHPAQmpQSPEAAGGTPGILLATDDI 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446335583  84 DALYSKLNDLGLT-GHDIAEMNGRRVFNFQDGQGNYFAV 121
Cdd:cd07263   80 DATYERLTAAGVTfVQEPTQMGGGRVANFRDPDGNLFAL 118
 
Name Accession Description Interval E-value
VOC_like cd07263
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 6-121 2.87e-29

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: 319924 [Multi-domain]  Cd Length: 120  Bit Score: 102.38  E-value: 2.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   6 QVMLYVDDVEKAKAFWTETLEFVVVSETPLaEDYVAVEVSPTKDAETSLTIMAKEFIEK--YSPEVNLGTPSLMFKEKNF 83
Cdd:cd07263    1 QVMLYVDDQDKALDFYVEKLGFEVVEDVPM-GGMRWVTVAPPGSPGTSLLLEPKAHPAQmpQSPEAAGGTPGILLATDDI 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446335583  84 DALYSKLNDLGLT-GHDIAEMNGRRVFNFQDGQGNYFAV 121
Cdd:cd07263   80 DATYERLTAAGVTfVQEPTQMGGGRVANFRDPDGNLFAL 118
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
3-121 4.77e-11

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 55.53  E-value: 4.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583    3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSETPLAEDYVAVEVSPTkDAETSLTIMAKEFIEKYSPEVNL-GTPSLMFKEK 81
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFL-AGGRVLELLLNETPPPAAAGFGGhHIAFIAFSVD 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 446335583   82 NFDALYSKLNDLGLTGHDIA--EMNGRRVFNFQDGQGNYFAV 121
Cdd:pfam00903  80 DVDAAYDRLKAAGVEIVREPgrHGWGGRYSYFRDPDGNLIEL 121
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 3-117 1.14e-10

Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 440115 [Multi-domain]  Cd Length: 125  Bit Score: 54.61  E-value: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSETPLAED---YVAVEVsptkDAETSLTIMAKEFIEKYSPEVNLGTpsLMFK 79
Cdd:COG0346    2 GLHHVTLRVSDLEASLAFYTDVLGLELVKRTDFGDGgfgHAFLRL----GDGTELELFEAPGAAPAPGGGGLHH--LAFR 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446335583  80 EKNFDALYSKLNDLGLT-GHDIAEM-NGRRVFNFQDGQGN 117
Cdd:COG0346   76 VDDLDAAYARLRAAGVEiEGEPRDRaYGYRSAYFRDPDGN 115
 
Name Accession Description Interval E-value
VOC_like cd07263
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 6-121 2.87e-29

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: 319924 [Multi-domain]  Cd Length: 120  Bit Score: 102.38  E-value: 2.87e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   6 QVMLYVDDVEKAKAFWTETLEFVVVSETPLaEDYVAVEVSPTKDAETSLTIMAKEFIEK--YSPEVNLGTPSLMFKEKNF 83
Cdd:cd07263    1 QVMLYVDDQDKALDFYVEKLGFEVVEDVPM-GGMRWVTVAPPGSPGTSLLLEPKAHPAQmpQSPEAAGGTPGILLATDDI 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 446335583  84 DALYSKLNDLGLT-GHDIAEMNGRRVFNFQDGQGNYFAV 121
Cdd:cd07263   80 DATYERLTAAGVTfVQEPTQMGGGRVANFRDPDGNLFAL 118
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
3-121 4.77e-11

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 55.53  E-value: 4.77e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583    3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSETPLAEDYVAVEVSPTkDAETSLTIMAKEFIEKYSPEVNL-GTPSLMFKEK 81
Cdd:pfam00903   1 RIDHVALRVGDLEKSLDFYTDVLGFKLVEETDAGEEGGLRSAFFL-AGGRVLELLLNETPPPAAAGFGGhHIAFIAFSVD 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 446335583   82 NFDALYSKLNDLGLTGHDIA--EMNGRRVFNFQDGQGNYFAV 121
Cdd:pfam00903  80 DVDAAYDRLKAAGVEIVREPgrHGWGGRYSYFRDPDGNLIEL 121
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 3-117 1.14e-10

Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 440115 [Multi-domain]  Cd Length: 125  Bit Score: 54.61  E-value: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSETPLAED---YVAVEVsptkDAETSLTIMAKEFIEKYSPEVNLGTpsLMFK 79
Cdd:COG0346    2 GLHHVTLRVSDLEASLAFYTDVLGLELVKRTDFGDGgfgHAFLRL----GDGTELELFEAPGAAPAPGGGGLHH--LAFR 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446335583  80 EKNFDALYSKLNDLGLT-GHDIAEM-NGRRVFNFQDGQGN 117
Cdd:COG0346   76 VDDLDAAYARLRAAGVEiEGEPRDRaYGYRSAYFRDPDGN 115
VOC COG3324
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 1-121 8.10e-10

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


Pssm-ID: 442553 [Multi-domain]  Cd Length: 119  Bit Score: 52.33  E-value: 8.10e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   1 MEKLNQVMLYVDDVEKAKAFWTETLEFVVVSETPLAEDYVAVEVSPTKDAEtsltIMAKEfiekYSPEVnlGTPSLMFKE 80
Cdd:COG3324    2 PGTIVWVELPVDDLERAKAFYEEVFGWTFEDDAGPGGDYAEFDTDGGQVGG----LMPGA----EEPGG--PGWLLYFAV 71

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 446335583  81 KNFDALYSKLNDLGLT-GHDIAEMNGR-RVFNFQDGQGNYFAV 121
Cdd:COG3324   72 DDLDAAVARVEAAGGTvLRPPTDIPPWgRFAVFRDPEGNRFGL 114
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 7-119 1.49e-04

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 is found in a variety of structurally related metalloproteins, including the type I extradiol dioxygenases, glyoxalase I and a group of antibiotic resistance proteins. 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). Type I extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into aromatic substrates, which results in the cleavage of aromatic rings. They are key enzymes in the degradation of aromatic compounds. Type I extradiol dioxygenases include class I and class II enzymes. Class I and II enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. Glyoxylase I catalyzes the glutathione-dependent inactivation of toxic methylglyoxal, requiring zinc or nickel ions for activity. The antibiotic resistance proteins in this family use a variety of mechanisms to block the function of antibiotics. Bleomycin resistance protein (BLMA) sequesters bleomycin's activity by directly binding to it. Whereas, three types of fosfomycin resistance proteins employ different mechanisms to render fosfomycin inactive by modifying the fosfomycin molecule. Although the proteins in this superfamily are functionally distinct, their structures are similar. The difference among the three dimensional structures of the three types of proteins in this superfamily is interesting from an evolutionary perspective. Both glyoxalase I and BLMA show domain swapping between subunits. However, there is no domain swapping for type 1 extradiol dioxygenases.


Pssm-ID: 319898 [Multi-domain]  Cd Length: 112  Bit Score: 38.27  E-value: 1.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   7 VMLYVDDVEKAKAFWTETLEFVVVSEtplAEDYVAVEVSPTKDAETSLTimakEFIEKySPEVNLGTPSLMFKEKNFDAL 86
Cdd:cd06587    2 VALRVPDLDASVAFYEEVLGFEVVSR---NEGGGFAFLRLGPGLRLALL----EGPEP-ERPGGGGLFHLAFEVDDVDEV 73

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 446335583  87 YSKLNDLGLTG----HDIAEMNGRRVFNFQDGQGNYF 119
Cdd:cd06587   74 DERLREAGAEGelvaPPVDDPWGGRSFYFRDPDGNLI 110
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
3-117 1.93e-04

Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 38.40  E-value: 1.93e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSETplaEDYVAVEVSPTkdaETSLTIMAKEFIEKYSPEVNLG-----TPSlm 77
Cdd:COG2514    3 RLGHVTLRVRDLERSAAFYTDVLGLEVVERE---GGRVYLRADGG---EHLLVLEEAPGAPPRPGAAGLDhvafrVPS-- 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 446335583  78 fkEKNFDALYSKLNDLGLTGHDIAEMNGRRVFNFQDGQGN 117
Cdd:COG2514   75 --RADLDAALARLAAAGVPVEGAVDHGVGESLYFRDPDGN 112
VOC_like cd09011
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 3-123 8.75e-03

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: 319953  Cd Length: 122  Bit Score: 33.60  E-value: 8.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446335583   3 KLNQVMLYVDDVEKAKAFWTETLEFVVVSEtpLAEDYVavevsptkdAETSLTIMAK----EFIEKYSPEVNLGTPS--L 76
Cdd:cd09011    2 KFVNPLLVVKDIEKSKKFYEDVLGQKILLD--FGENVV---------FEGGFALQEKkswlETIIISDLSIKQQSNNfeL 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446335583  77 MFKEKNFDALYSKLNDLGLTG--HDIAEMN-GRRVFNFQDGQGNYFAVSD 123
Cdd:cd09011   71 YFEVDDFDAFFEKLNPHKDIEfiHPILEHPwGQRVFRFYDPDGHIIEIGE 120
 
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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