NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|489529944|ref|WP_003434678|]
View 

VOC family protein [Clostridioides difficile]

Protein Classification

VOC family protein( domain architecture ID 10001243)

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 14-117 4.11e-09

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: 50.38  E-value: 4.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944  14 DIEKAIPFYENLLKEKCSLRFSYKEVGLELA--QIGN--VLLLSGSDDAlKPFIETKST----FMVDSVDEWRSYLLDNG 85
Cdd:COG0346   12 DLEASLAFYTDVLGLELVKRTDFGDGGFGHAflRLGDgtELELFEAPGA-APAPGGGGLhhlaFRVDDLDAAYARLRAAG 90

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489529944  86 AVVVRDKKKVPTGYNMT-LRHPDGTIIEYVQHT 117
Cdd:COG0346   91 VEIEGEPRDRAYGYRSAyFRDPDGNLIELVEPP 123
 
Name Accession Description Interval E-value
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 14-117 4.11e-09

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: 50.38  E-value: 4.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944  14 DIEKAIPFYENLLKEKCSLRFSYKEVGLELA--QIGN--VLLLSGSDDAlKPFIETKST----FMVDSVDEWRSYLLDNG 85
Cdd:COG0346   12 DLEASLAFYTDVLGLELVKRTDFGDGGFGHAflRLGDgtELELFEAPGA-APAPGGGGLhhlaFRVDDLDAAYARLRAAG 90

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489529944  86 AVVVRDKKKVPTGYNMT-LRHPDGTIIEYVQHT 117
Cdd:COG0346   91 VEIEGEPRDRAYGYRSAyFRDPDGNLIELVEPP 123
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 8-113 4.05e-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: 37.12  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944   8 TRFYIQDIEKAIPFYENLLKEKCSLRF-SYKEVGLELAQIGNVLLLSGSDDALKPF-------IETKStfmVDSVDEWRS 79
Cdd:cd06587    2 VALRVPDLDASVAFYEEVLGFEVVSRNeGGGFAFLRLGPGLRLALLEGPEPERPGGgglfhlaFEVDD---VDEVDERLR 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489529944  80 YLLDNGAVVVRDKKKVPTGYNMTLRHPDGTIIEY 113
Cdd:cd06587   79 EAGAEGELVAPPVDDPWGGRSFYFRDPDGNLIEF 112
 
Name Accession Description Interval E-value
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 14-117 4.11e-09

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: 50.38  E-value: 4.11e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944  14 DIEKAIPFYENLLKEKCSLRFSYKEVGLELA--QIGN--VLLLSGSDDAlKPFIETKST----FMVDSVDEWRSYLLDNG 85
Cdd:COG0346   12 DLEASLAFYTDVLGLELVKRTDFGDGGFGHAflRLGDgtELELFEAPGA-APAPGGGGLhhlaFRVDDLDAAYARLRAAG 90

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489529944  86 AVVVRDKKKVPTGYNMT-LRHPDGTIIEYVQHT 117
Cdd:COG0346   91 VEIEGEPRDRAYGYRSAyFRDPDGNLIELVEPP 123
VOC COG3324
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 8-116 4.06e-08

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


Pssm-ID: 442553 [Multi-domain]  Cd Length: 119  Bit Score: 47.71  E-value: 4.06e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944   8 TRFYIQDIEKAIPFYENLL----KEKCSLRFSYKEVGLELAQIGnvLLLSGSDDALKPFIETksTFMVDSVDEWRSYLLD 83
Cdd:COG3324    8 VELPVDDLERAKAFYEEVFgwtfEDDAGPGGDYAEFDTDGGQVG--GLMPGAEEPGGPGWLL--YFAVDDLDAAVARVEA 83

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489529944  84 NGAVVVRDKKKVP-TGYNMTLRHPDGTIIEYVQH 116
Cdd:COG3324   84 AGGTVLRPPTDIPpWGRFAVFRDPEGNRFGLWQP 117
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 8-113 4.05e-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: 37.12  E-value: 4.05e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944   8 TRFYIQDIEKAIPFYENLLKEKCSLRF-SYKEVGLELAQIGNVLLLSGSDDALKPF-------IETKStfmVDSVDEWRS 79
Cdd:cd06587    2 VALRVPDLDASVAFYEEVLGFEVVSRNeGGGFAFLRLGPGLRLALLEGPEPERPGGgglfhlaFEVDD---VDEVDERLR 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489529944  80 YLLDNGAVVVRDKKKVPTGYNMTLRHPDGTIIEY 113
Cdd:cd06587   79 EAGAEGELVAPPVDDPWGGRSFYFRDPDGNLIEF 112
MMCE cd07249
Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) ...
 14-115 6.01e-04

Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases.


Pssm-ID: 319912 [Multi-domain]  Cd Length: 127  Bit Score: 36.79  E-value: 6.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944  14 DIEKAIPFYENLLKEKCSLRFSYKEVGLELA--QIGNV---LLLSGSDDA-LKPFIETKS------TFMVDSVDEWRSYL 81
Cdd:cd07249   10 DLDEALKFYEDVLGVKVSEPEELEEQGVRVAflELGNTqieLLEPLGEDSpIAKFLDKKGgglhhiAFEVDDIDAAVEEL 89

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489529944  82 LDNGAVVVRDKKKVPTGYN--MTLrHPD---GTIIEYVQ 115
Cdd:cd07249   90 KAQGVRLLSEGPRIGAHGKrvAFL-HPKdtgGVLIELVE 127
VOC_like cd08354
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 8-112 2.93e-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: 319942  Cd Length: 122  Bit Score: 35.03  E-value: 2.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489529944   8 TRFYIQDIEKAIPFYENLLKEKCsLRFSYKEVGLELAqiGNVLLL-----SGSDDALKPF------IETKSTFMV--DSV 74
Cdd:cd08354    4 TCLYADDLDAAEAFYEDVLGLKP-MLRSGRHAFFRLG--PQVLLVfdpgaTSKDVRTGEVpghgasGHGHFAFAVptEEL 80

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 489529944  75 DEWRSYLLDNGAVVVRDKKKVPTGYNMTLRHPDGTIIE 112
Cdd:cd08354   81 AAWEARLEAKGVPIESYTQWPEGGKSLYFRDPAGNLVE 118
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH