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Conserved domains on  [gi|752559499|ref|WP_041230728|]
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VOC family protein [Deinococcus peraridilitoris]

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 ...
 6-130 3.75e-40

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 cd07235:

Pssm-ID: 472697  Cd Length: 123  Bit Score: 130.31  E-value: 3.75e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   6 DMVGYVVRDMQATLDFYRQLGLPIPENAHLNPagesemHVEVTV-SGYRLAWDDLALIRQLDSSWEEPR-GRRISVAFKT 83
Cdd:cd07235    2 SLIAIVVEDMAKSLEFYRKLGFEVPEEADSAP------HTEAALpGGIRLALDTEETIRSYDPGWQAPTgGGRFAIAFLC 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 752559499  84 DSPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLF 130
Cdd:cd07235   76 PTPAEVDAKYAELTGAGYEGHLKPWNAPWGQRYAIVKDPDGNVVDLF 122
 
Name Accession Description Interval E-value
MRD cd07235
Mitomycin C resistance protein (MRD); Mitomycin C (MC) is a naturally occurring antibiotic, ...
 6-130 3.75e-40

Mitomycin C resistance protein (MRD); Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance protein, glyoxalase I, and extradiol dioxygenases; and it has binding sites at an identical location to binding sites in these evolutionarily related enzymes.


Pssm-ID: 319901  Cd Length: 123  Bit Score: 130.31  E-value: 3.75e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   6 DMVGYVVRDMQATLDFYRQLGLPIPENAHLNPagesemHVEVTV-SGYRLAWDDLALIRQLDSSWEEPR-GRRISVAFKT 83
Cdd:cd07235    2 SLIAIVVEDMAKSLEFYRKLGFEVPEEADSAP------HTEAALpGGIRLALDTEETIRSYDPGWQAPTgGGRFAIAFLC 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 752559499  84 DSPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLF 130
Cdd:cd07235   76 PTPAEVDAKYAELTGAGYEGHLKPWNAPWGQRYAIVKDPDGNVVDLF 122
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
6-129 1.21e-17

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 72.87  E-value: 1.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499    6 DMVGYVVRDMQATLDFYRQ-LGLPIPENAHlNPAGESEMHVEVTVSGYRLAWDDLALIRQLDSSWEeprgrRISVAFKTD 84
Cdd:pfam00903   3 DHVALRVGDLEKSLDFYTDvLGFKLVEETD-AGEEGGLRSAFFLAGGRVLELLLNETPPPAAAGFG-----GHHIAFIAF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 752559499   85 SPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDL 129
Cdd:pfam00903  77 SVDDVDAAYDRLKAAGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
11-132 1.41e-17

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 72.58  E-value: 1.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  11 VVRDMQATLDFYRQ-LGLPIpENAHLNPAGEsEMHVEVTVSGYRLAWDDLAlirqldSSWEEPRGRRISVAFKTDspaEV 89
Cdd:COG2764    7 VVDDAEEALEFYEDvFGFEV-VFRMTDPDGK-IMHAELRIGGSVLMLSDAP------PDSPAAEGNGVSLSLYVD---DV 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 752559499  90 DALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLFCA 132
Cdd:COG2764   76 DALFARLVAAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINTP 118
 
Name Accession Description Interval E-value
MRD cd07235
Mitomycin C resistance protein (MRD); Mitomycin C (MC) is a naturally occurring antibiotic, ...
 6-130 3.75e-40

Mitomycin C resistance protein (MRD); Mitomycin C (MC) is a naturally occurring antibiotic, and antitumor agent used in the treatment of cancer. Its antitumor activity is exerted primarily through monofunctional and bifunctional alkylation of DNA. MRD binds to MC and functions as a component of the MC exporting system. MC is bound to MRD by a stacking interaction between a His and a Trp. MRD adopts a structural fold similar to bleomycin resistance protein, glyoxalase I, and extradiol dioxygenases; and it has binding sites at an identical location to binding sites in these evolutionarily related enzymes.


Pssm-ID: 319901  Cd Length: 123  Bit Score: 130.31  E-value: 3.75e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   6 DMVGYVVRDMQATLDFYRQLGLPIPENAHLNPagesemHVEVTV-SGYRLAWDDLALIRQLDSSWEEPR-GRRISVAFKT 83
Cdd:cd07235    2 SLIAIVVEDMAKSLEFYRKLGFEVPEEADSAP------HTEAALpGGIRLALDTEETIRSYDPGWQAPTgGGRFAIAFLC 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 752559499  84 DSPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLF 130
Cdd:cd07235   76 PTPAEVDAKYAELTGAGYEGHLKPWNAPWGQRYAIVKDPDGNVVDLF 122
Glyoxalase pfam00903
Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;
6-129 1.21e-17

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;


Pssm-ID: 395724 [Multi-domain]  Cd Length: 121  Bit Score: 72.87  E-value: 1.21e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499    6 DMVGYVVRDMQATLDFYRQ-LGLPIPENAHlNPAGESEMHVEVTVSGYRLAWDDLALIRQLDSSWEeprgrRISVAFKTD 84
Cdd:pfam00903   3 DHVALRVGDLEKSLDFYTDvLGFKLVEETD-AGEEGGLRSAFFLAGGRVLELLLNETPPPAAAGFG-----GHHIAFIAF 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 752559499   85 SPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDL 129
Cdd:pfam00903  77 SVDDVDAAYDRLKAAGVEIVREPGRHGWGGRYSYFRDPDGNLIEL 121
PhnB COG2764
Zn-dependent glyoxalase, PhnB family [Energy production and conversion];
11-132 1.41e-17

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


Pssm-ID: 442048 [Multi-domain]  Cd Length: 118  Bit Score: 72.58  E-value: 1.41e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  11 VVRDMQATLDFYRQ-LGLPIpENAHLNPAGEsEMHVEVTVSGYRLAWDDLAlirqldSSWEEPRGRRISVAFKTDspaEV 89
Cdd:COG2764    7 VVDDAEEALEFYEDvFGFEV-VFRMTDPDGK-IMHAELRIGGSVLMLSDAP------PDSPAAEGNGVSLSLYVD---DV 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 752559499  90 DALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLFCA 132
Cdd:COG2764   76 DALFARLVAAGATVVMPLQDTFWGDRFGMVRDPFGVLWMINTP 118
GloA COG0346
Catechol 2,3-dioxygenase or related enzyme, vicinal oxygen chelate (VOC) family [Secondary ...
 6-131 4.39e-16

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: 69.25  E-value: 4.39e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   6 DMVGYVVRDMQATLDFYRQ-LGLPipENAHLNPAGESEMHVEVTVSGyrlaWDDLALIRQLDSSWEEPRGRRISVAFKTD 84
Cdd:COG0346    4 HHVTLRVSDLEASLAFYTDvLGLE--LVKRTDFGDGGFGHAFLRLGD----GTELELFEAPGAAPAPGGGGLHHLAFRVD 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 752559499  85 spaEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLFC 131
Cdd:COG0346   78 ---DLDAAYARLRAAGVEIEGEPRDRAYGYRSAYFRDPDGNLIELVE 121
COG3607 COG3607
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 12-125 1.11e-14

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


Pssm-ID: 442825  Cd Length: 126  Bit Score: 65.62  E-value: 1.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  12 VRDMQATLDFYRQLGLPIpenahlNPAGESEMHVEVTVS-GYRLAWDDLALIRQlDSSWE---EPRGRRISVAFKTDSPA 87
Cdd:COG3607   11 VADLERSRAFYEALGFTF------NPQFSDEGAACFVLGeGIVLMLLPREKFAT-FTGKPiadATGFTEVLLALNVESRE 83

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 752559499  88 EVDALYDKLTALGYSGHTPPYNAFWGqRYAVVYDPDGN 125
Cdd:COG3607   84 EVDALVAKALAAGGTVLKPPQDVGGM-YSGYFADPDGH 120
VOC_like cd07264
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 12-130 1.53e-14

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: 319925 [Multi-domain]  Cd Length: 118  Bit Score: 65.05  E-value: 1.53e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  12 VRDMQATLDFYR-QLGLPIpenAHLNPAGESemhVEVTVSGYRLAWDDLALIRQLDSSweEPRGRRISVAFKTDSpaeVD 90
Cdd:cd07264    8 VDDFAASLRFYRdVLGLPP---RFLHEEGEY---AEFDTGETKLALFSRKEMARSGGP--DRRGSAFELGFEVDD---VE 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 752559499  91 ALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLF 130
Cdd:cd07264   77 ATVEELVERGAEFVREPANKPWGQTVAYVRDPDGNLIEIC 116
VOC cd06587
vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate (VOC) superfamily is composed ...
 8-129 9.26e-13

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: 60.23  E-value: 9.26e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYRQ-LGLPIpenahlnpageSEMHVEVTVSGYRLAWDDLALIRQLDSSWEEPRGRRISVAFKTDSP 86
Cdd:cd06587    2 VALRVPDLDASVAFYEEvLGFEV-----------VSRNEGGGFAFLRLGPGLRLALLEGPEPERPGGGGLFHLAFEVDDV 70

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 752559499  87 AEVDALYDKLTALGYsGHTPPYNAFWGQRYAVVYDPDGNTVDL 129
Cdd:cd06587   71 DEVDERLREAGAEGE-LVAPPVDDPWGGRSFYFRDPDGNLIEF 112
PsjN_like cd16356
Burkholderia Phytofirmans glyoxalase/bleomycin resistance protein/dioxygenase family enzyme ...
 13-129 8.38e-11

Burkholderia Phytofirmans glyoxalase/bleomycin resistance protein/dioxygenase family enzyme and similar proteins; Burkholderia Phytofirmans glyoxalase/bleomycin resistance protein/dioxygenase family enzyme and similar proteins. 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: 319963  Cd Length: 119  Bit Score: 55.12  E-value: 8.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  13 RDMQATLDFYRQL-GLP-IPENAhlnpageSEMHVEVTVSGYRL------AWDDLALIRQLDSSweeprGRRISVAFKTD 84
Cdd:cd16356    7 ADIVALSDFYSELfGLEeIFEIR-------SPIFRGLRTGDSCLgfnapeAYELLGLPEFSDTP-----GIRILLTFDVD 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 752559499  85 SPAEVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDL 129
Cdd:cd16356   75 DVEAVDRLVPRAAALGATLIKPPYDTYYGWYQAVLLDPEGNVFRI 119
VOC COG3324
Lactoylglutathione lyase-related enzyme, vicinal oxygen chelate (VOC) family [General function ...
 1-130 2.14e-10

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


Pssm-ID: 442553 [Multi-domain]  Cd Length: 119  Bit Score: 54.26  E-value: 2.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   1 MSVTPDMVGYVVRDMQATLDFYRQ-LGLPIPENAHLNPagesemhvevtvsGYRLAWDDLALIRQLDSSWEEPRGRRISV 79
Cdd:COG3324    1 MPGTIVWVELPVDDLERAKAFYEEvFGWTFEDDAGPGG-------------DYAEFDTDGGQVGGLMPGAEEPGGPGWLL 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 752559499  80 AFKTDSpaeVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVDLF 130
Cdd:COG3324   68 YFAVDD---LDAAVARVEAAGGTVLRPPTDIPPWGRFAVFRDPEGNRFGLW 115
CatE COG2514
Catechol-2,3-dioxygenase [Secondary metabolites biosynthesis, transport and catabolism];
8-131 8.47e-09

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


Pssm-ID: 442004 [Multi-domain]  Cd Length: 141  Bit Score: 50.34  E-value: 8.47e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYRQ-LGLPipenahlnPAGESEMHVEVTVSGyrlAWDDLALIRQLDSSWEEPRGRRISVAFKTDSP 86
Cdd:COG2514    7 VTLRVRDLERSAAFYTDvLGLE--------VVEREGGRVYLRADG---GEHLLVLEEAPGAPPRPGAAGLDHVAFRVPSR 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 752559499  87 AEVDALYDKLTALGYSgHTPPYNaFWGQRYAVVYDPDGNTVDLFC 131
Cdd:COG2514   76 ADLDAALARLAAAGVP-VEGAVD-HGVGESLYFRDPDGNLIELYT 118
VOC_like cd07251
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 12-124 1.40e-08

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: 319914 [Multi-domain]  Cd Length: 120  Bit Score: 49.60  E-value: 1.40e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  12 VRDMQATLDFYRQLGLPIpenahlNPAGESEMhVEVTVSGYRLA---WDDLAliRQLDSSWEEPRGRRISVAFKTDSPAE 88
Cdd:cd07251    6 VRDLERSARFYEALGWKP------NLDPNDGV-VFFQLGGTVLAlypRDALA--EDAGVSVTGAGFSGVTLAHNVRSREE 76

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 752559499  89 VDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDG 124
Cdd:cd07251   77 VDQLLAKAVAAGGKILKPPQEVFWGGYSGYFADPDG 112
VOC_like cd07262
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 8-131 4.55e-08

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: 319923 [Multi-domain]  Cd Length: 121  Bit Score: 47.99  E-value: 4.55e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYRQLglpipenahLNPAGESEMHVEVTVSGYRLAWDDLALIRQLDSSWEEPRGRRISVAFKTDSPA 87
Cdd:cd07262    4 VTIGVNDLERSRAFYDAA---------LAPLGYKRGFEDGGRVGYGLEGGPDFWVTEPFDGEPATAGNGTHVAFAAPSRA 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 752559499  88 EVDALYDKLTALGYSGH-TPPYNAFWGQRY--AVVYDPDGNTVDLFC 131
Cdd:cd07262   75 AVDAFHAAALAAGGTDNgAPGLRPHYHPGYyaAYVRDPDGNKIEAVC 121
BLMA_like cd08349
Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance ...
 12-125 5.53e-08

Bleomycin binding protein (BLMA) and similar proteins; BLMA also called Bleomycin resistance protein, confers Bm resistance by directly binding to Bm. Bm is a glycopeptide antibiotic produced naturally by actinomycetes. It is a potent anti-cancer drug, which acts as a strong DNA-cutting agent, thereby causing cell death. BLMA is produced by actinomycetes to protect themselves against their own lethal compound. BLMA has two identically-folded subdomains, with the same alpha/beta fold; these two halves have no sequence similarity. BLMAs are dimers and each dimer binds to two Bm molecules at the Bm-binding pockets formed at the dimer interface; two Bm molecules are bound per dimer. BLMA 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. As for the larger superfamily, this family contains members with or without domain swapping.


Pssm-ID: 319937 [Multi-domain]  Cd Length: 114  Bit Score: 47.61  E-value: 5.53e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  12 VRDMQATLDFYRQ-LGLpipenahlnpagesEMHVEVTVSGY-RLAWDDLAL-IRQLDSswEEPRGRRISVAFKTDSpae 88
Cdd:cd08349    6 VRDIDKTLAFYVDvLGF--------------EVDYERPPPGYaILSRGGVELhLFEHPG--LDPAGSGVAAYIRVED--- 66

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 752559499  89 VDALYDKLTALGYSG-----HTPPYNAFWGQRYAVVYDPDGN 125
Cdd:cd08349   67 IDALHAELKAAGLPLfgiprITPIEDKPWGMREFAVVDPDGN 108
VOC_like cd07263
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 8-129 7.04e-06

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: 42.28  E-value: 7.04e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYR-QLGLpipENAHLNPAGEsemHVEVTV-----SGYRLAWDDLALIRQLDSSWEEPRGRRiSVAF 81
Cdd:cd07263    2 VMLYVDDQDKALDFYVeKLGF---EVVEDVPMGG---MRWVTVappgsPGTSLLLEPKAHPAQMPQSPEAAGGTP-GILL 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 752559499  82 KTDspaEVDALYDKLTALGYSGHTPPyNAFWGQRYAVVYDPDGNTVDL 129
Cdd:cd07263   75 ATD---DIDATYERLTAAGVTFVQEP-TQMGGGRVANFRDPDGNLFAL 118
VOC_like cd07246
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 2-126 5.67e-05

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: 39.97  E-value: 5.67e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   2 SVTPDMVgyvVRDMQATLDFYRQLgLPIPENAHLNPAGESEMHVEVTVSGYRLAWDDLALIRQLDSSWEEPrGRRISVAF 81
Cdd:cd07246    2 TVSPYLV---VEDAAAAIAFYKKA-FGAEELGRTTQEDGRVGHAELRIGGTVVMVADENPERGALSPTKLG-GTPVIFHL 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 752559499  82 KTDSpaeVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNT 126
Cdd:cd07246   77 YVED---VDATFARAVAAGAVVVEPVEDQFWGDRVGKVKDPFGHV 118
ED_TypeI_classII_N cd16360
N-terminal domain of type I, class II extradiol dioxygenases; This family contains the ...
 8-130 1.68e-04

N-terminal domain of type I, class II extradiol dioxygenases; This family contains the N-terminal non-catalytic domain of type I, class II extradiol dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site; extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon, whereas intradiol enzymes cleave the aromatic ring between two hydroxyl groups. Extradiol dioxygenases are classified into type I and type II enzymes. Type I extradiol dioxygenases include class I and class II enzymes. These two classes of enzymes show sequence similarity; the two-domain class II enzymes evolved from a class I enzyme through gene duplication. The extradiol dioxygenases represented in this family are type I, class II enzymes, and are composed of the N- and C-terminal domains of similar structure fold, resulting from an ancient gene duplication. The active site is located in a funnel-shaped space of the C-terminal domain. A catalytically essential metal, Fe(II) or Mn(II), presents in all the enzymes in this family.


Pssm-ID: 319967  Cd Length: 111  Bit Score: 38.45  E-value: 1.68e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYRQ-LGLpipenahlNPAGESEMHVevtvsgYRLAWDDLALIRQLdssWEEPRGRRISVAFKTDSP 86
Cdd:cd16360    2 AELGVPDLEKALEFYTDvLGL--------QVAKRDGNSV------YLRGYEDEHHSLVL---YEAPEAGLKHFAFEVASE 64

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 752559499  87 AEVDALYDKLTALGYSGHTPPYNAFWGQRYAV-VYDPDGNTVDLF 130
Cdd:cd16360   65 EDLERAAASLTALGCDVTWGPDGEVPGGGKGFrFQDPSGHLLELF 109
PhnB_like cd06588
Escherichia coli PhnB and similar proteins; The Escherichia coli phnB gene is found next to an ...
 30-122 2.59e-04

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: 38.02  E-value: 2.59e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499  30 PENAHLNPAGESE--MHVEVTVSGYRLawddLALirqlDSSWEEPR--GRRISVAFKTDSPAEVDALYDKLTAlgySGHT 105
Cdd:cd06588   34 GEGPPDFPEGDEGkvMHAEFTLGGQTL----MAS----DDGPGFPFtfGNAISLSVDCDSQEEADRLFEKLSE---GGEV 102

                         90
                 ....*....|....*....
gi 752559499 106 --PPYNAFWGQRYAVVYDP 122
Cdd:cd06588  103 lmPLQETFWGARYGWVKDK 121
VOC_like cd08359
uncharacterized subfamily of vicinal oxygen chelate (VOC) family; The vicinal oxygen chelate ...
 88-128 1.71e-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: 319947 [Multi-domain]  Cd Length: 119  Bit Score: 35.84  E-value: 1.71e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 752559499  88 EVDALYDKLTALGYSGHTPPYNAFWGQRYAVVYDPDGNTVD 128
Cdd:cd08359   76 DADAEYERLTQAGLEFLEPPRDEPWGQRRFIVRDPNGVLID 116
MMCE cd07249
Methylmalonyl-CoA epimerase (MMCE); MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) ...
 6-127 3.62e-03

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: 34.86  E-value: 3.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   6 DMVGYVVRDMQATLDFYRQ-LGLPIPENahlnpagESEMHVEVTVSGYRLAWDDLALIRQL--DSSW----EEPRGRRIS 78
Cdd:cd07249    2 DHIGIAVPDLDEALKFYEDvLGVKVSEP-------EELEEQGVRVAFLELGNTQIELLEPLgeDSPIakflDKKGGGLHH 74

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 752559499  79 VAFKTDSpaeVDALYDKLTALGY-SGHTPPYNAFWGQRYAVVYDPDGNTV 127
Cdd:cd07249   75 IAFEVDD---IDAAVEELKAQGVrLLSEGPRIGAHGKRVAFLHPKDTGGV 121
BphC5-RrK37_N_like cd08362
N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from ...
 8-129 9.98e-03

N-terminal, non-catalytic, domain of BphC5 (2,3-dihydroxybiphenyl 1,2-dioxygenase) from Rhodococcus rhodochrous K37, and similar proteins; 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC) catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). The enzyme contains a N-terminal and a C-terminal domain of similar structure fold, resulting from an ancient gene duplication. BphC belongs to the type I extradiol dioxygenase family, which requires a metal in the active site for its catalytic activity. Polychlorinated biphenyl degrading bacteria demonstrate multiplicity of BphCs. Bacterium Rhodococcus rhodochrous K37 has eight genes encoding BphC enzymes. This family includes the N-terminal domain of BphC5-RrK37. The crystal structure of the protein from Novosphingobium aromaticivorans has a Mn(II)in the active site, although most proteins of type I extradiol dioxygenases are activated by Fe(II).


Pssm-ID: 319950 [Multi-domain]  Cd Length: 120  Bit Score: 33.76  E-value: 9.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 752559499   8 VGYVVRDMQATLDFYRQL-GL----PIPENAHLNPAGeSEMHVevtvsgyrlawddLALiRQLDssweEPRGRRISvaFK 82
Cdd:cd08362    7 VALGVPDLAAEREFYTEVwGLeevaEDDDVVYLRAEG-SEHHV-------------LRL-RQSD----ENRLDLIA--FA 65

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 752559499  83 TDSPAEVDALYDKLTALGYS-GHTPPYNAFWGQRYAV-VYDPDGNTVDL 129
Cdd:cd08362   66 AATRADVDALAARLAAAGVRiLSEPGPLDDPGGGYGFrFFDPDGRTIEV 114
 
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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