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Conserved domains on  [gi|446256662|ref|WP_000334517|]
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MULTISPECIES: hypothetical 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 ...
 3-116 3.24e-08

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 cd08346:

Pssm-ID: 472697  Cd Length: 124  Bit Score: 51.13  E-value: 3.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGL-------NYEELLENSIRFGDADISPGTRLQFIQVP--SEQLEESHFVG-IGLRT 72
Cdd:cd08346    1 GIHHITAITGDAQENVDFYVKVLGLrlvkktvNQDDPPMYHLYYGDELGSPGTLLTFFPWPlgGPGRRGTGQISrIGLRV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446256662  73 PTDSgLEEYAEILSNKDIPFTTVKELNGNKYFSLEDNNGHIFSI 116
Cdd:cd08346   81 PKGS-LSFWAERLEKFGVPHSEVVTRFGEKYLRFEDPDGTRLFL 123
VOC super family cl14632
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 144-241 1.29e-06

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 cd08347:

Pssm-ID: 472697  Cd Length: 157  Bit Score: 47.24  E-value: 1.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662 144 GLGPVILKVNHVDITGQILTNIFGLEVFAEYqpfdnaDYHVQVFKVGTGGlGGEIHLMPVETEMT-MPECGAVDQVEFET 222
Cdd:cd08347    1 GLHGVTLTVREPEETDAFLTNVFGFTEVGEE------GDLVRLFAGGNGS-GGVVDVLDDPDLPSaQQGYGTVHHVAFRV 73

                         90
                 ....*....|....*....
gi 446256662 223 KDADFFNQAKSRLDEVEIP 241
Cdd:cd08347   74 ADDEEQAAWKERLEELGFD 92
 
Name Accession Description Interval E-value
PcpA_N_like cd08346
N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase ...
 3-116 3.24e-08

N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; The N-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.


Pssm-ID: 319934  Cd Length: 124  Bit Score: 51.13  E-value: 3.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGL-------NYEELLENSIRFGDADISPGTRLQFIQVP--SEQLEESHFVG-IGLRT 72
Cdd:cd08346    1 GIHHITAITGDAQENVDFYVKVLGLrlvkktvNQDDPPMYHLYYGDELGSPGTLLTFFPWPlgGPGRRGTGQISrIGLRV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446256662  73 PTDSgLEEYAEILSNKDIPFTTVKELNGNKYFSLEDNNGHIFSI 116
Cdd:cd08346   81 PKGS-LSFWAERLEKFGVPHSEVVTRFGEKYLRFEDPDGTRLFL 123
PcpA_C_like cd08347
C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase ...
 144-241 1.29e-06

C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.


Pssm-ID: 319935  Cd Length: 157  Bit Score: 47.24  E-value: 1.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662 144 GLGPVILKVNHVDITGQILTNIFGLEVFAEYqpfdnaDYHVQVFKVGTGGlGGEIHLMPVETEMT-MPECGAVDQVEFET 222
Cdd:cd08347    1 GLHGVTLTVREPEETDAFLTNVFGFTEVGEE------GDLVRLFAGGNGS-GGVVDVLDDPDLPSaQQGYGTVHHVAFRV 73

                         90
                 ....*....|....*....
gi 446256662 223 KDADFFNQAKSRLDEVEIP 241
Cdd:cd08347   74 ADDEEQAAWKERLEELGFD 92
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
3-118 8.12e-06

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


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 44.56  E-value: 8.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGLNYEELLENSIRFGDAdiSPGTRLQFIQVPSEQLEESH--FVGIGLRTPTDSGLEE 80
Cdd:COG2514    3 RLGHVTLRVRDLERSAAFYTDVLGLEVVEREGGRVYLRAD--GGEHLLVLEEAPGAPPRPGAagLDHVAFRVPSRADLDA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446256662  81 YAEILSNKDIPFTTVKELNGNKYFSLEDNNGHIFSIYS 118
Cdd:COG2514   81 ALARLAAAGVPVEGAVDHGVGESLYFRDPDGNLIELYT 118
 
Name Accession Description Interval E-value
PcpA_N_like cd08346
N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase ...
 3-116 3.24e-08

N-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; The N-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.


Pssm-ID: 319934  Cd Length: 124  Bit Score: 51.13  E-value: 3.24e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGL-------NYEELLENSIRFGDADISPGTRLQFIQVP--SEQLEESHFVG-IGLRT 72
Cdd:cd08346    1 GIHHITAITGDAQENVDFYVKVLGLrlvkktvNQDDPPMYHLYYGDELGSPGTLLTFFPWPlgGPGRRGTGQISrIGLRV 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 446256662  73 PTDSgLEEYAEILSNKDIPFTTVKELNGNKYFSLEDNNGHIFSI 116
Cdd:cd08346   81 PKGS-LSFWAERLEKFGVPHSEVVTRFGEKYLRFEDPDGTRLFL 123
PcpA_C_like cd08347
C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase ...
 144-241 1.29e-06

C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.


Pssm-ID: 319935  Cd Length: 157  Bit Score: 47.24  E-value: 1.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662 144 GLGPVILKVNHVDITGQILTNIFGLEVFAEYqpfdnaDYHVQVFKVGTGGlGGEIHLMPVETEMT-MPECGAVDQVEFET 222
Cdd:cd08347    1 GLHGVTLTVREPEETDAFLTNVFGFTEVGEE------GDLVRLFAGGNGS-GGVVDVLDDPDLPSaQQGYGTVHHVAFRV 73

                         90
                 ....*....|....*....
gi 446256662 223 KDADFFNQAKSRLDEVEIP 241
Cdd:cd08347   74 ADDEEQAAWKERLEELGFD 92
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
3-118 8.12e-06

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


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 44.56  E-value: 8.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGLNYEELLENSIRFGDAdiSPGTRLQFIQVPSEQLEESH--FVGIGLRTPTDSGLEE 80
Cdd:COG2514    3 RLGHVTLRVRDLERSAAFYTDVLGLEVVEREGGRVYLRAD--GGEHLLVLEEAPGAPPRPGAagLDHVAFRVPSRADLDA 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 446256662  81 YAEILSNKDIPFTTVKELNGNKYFSLEDNNGHIFSIYS 118
Cdd:COG2514   81 ALARLAAAGVPVEGAVDHGVGESLYFRDPDGNLIELYT 118
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 3-122 3.46e-05

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: 42.29  E-value: 3.46e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGL------NYEELLENSIRFGDADispGTRLQFIQVPSEQLEESH--FVGIGLRTPT 74
Cdd:COG0346    2 GLHHVTLRVSDLEASLAFYTDVLGLelvkrtDFGDGGFGHAFLRLGD---GTELELFEAPGAAPAPGGggLHHLAFRVDD 78

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 446256662  75 dsgLEEYAEILSNKDIPFTT--VKELNGNKYFSLEDNNGHIFSIYSNENN 122
Cdd:COG0346   79 ---LDAAYARLRAAGVEIEGepRDRAYGYRSAYFRDPDGNLIELVEPPPG 125
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 6-114 5.39e-05

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: 41.74  E-value: 5.39e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   6 SITLGTTNIEQTKHFMVDILGLnyEELLEN-SIRFGDADISPGTRLQFIQVPSEQLE-ESHFVGIGLRTPTDSGLEEYAE 83
Cdd:cd06587    1 HVALRVPDLDASVAFYEEVLGF--EVVSRNeGGGFAFLRLGPGLRLALLEGPEPERPgGGGLFHLAFEVDDVDEVDERLR 78

                         90       100       110
                 ....*....|....*....|....*....|..
gi 446256662  84 ILSNKDIPFTT-VKELNGNKYFSLEDNNGHIF 114
Cdd:cd06587   79 EAGAEGELVAPpVDDPWGGRSFYFRDPDGNLI 110
PcpA_C_like cd08347
C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase ...
 3-104 5.69e-03

C-terminal domain of Sphingobium chlorophenolicum 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins; The C-terminal domain of Sphingobium chlorophenolicum (formerly Sphingomonas chlorophenolica) 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA), and similar proteins. PcpA is a key enzyme in the pentachlorophenol (PCP) degradation pathway, catalyzing the conversion of 2,6-dichloro-p-hydroquinone to 2-chloromaleylacetate. This domain belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases.


Pssm-ID: 319935  Cd Length: 157  Bit Score: 36.45  E-value: 5.69e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446256662   3 GLRSITLGTTNIEQTKHFMVDILGLNYEELLENSIRFGDADISPGtrlQFIQVPSEQLEESHFVGIG------LRTPTDS 76
Cdd:cd08347    1 GLHGVTLTVREPEETDAFLTNVFGFTEVGEEGDLVRLFAGGNGSG---GVVDVLDDPDLPSAQQGYGtvhhvaFRVADDE 77

                         90       100
                 ....*....|....*....|....*...
gi 446256662  77 GLEEYAEILSNKDIPFTTVKELNgnkYF 104
Cdd:cd08347   78 EQAAWKERLEELGFDNSGIVDRF---YF 102
 
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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