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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  11 LNGLRHLALLVPNLEECERFYVDVLGMEVLNRaNEDLVYLTCGNDNLSL----GRAHAASNGLQTMDHYGFVVDSVEELE 86
Cdd:COG2514    1 ITRLGHVTLRVRDLERSAAFYTDVLGLEVVER-EGGRVYLRADGGEHLLvleeAPGAPPRPGAAGLDHVAFRVPSRADLD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489189306  87 AWYRYLKALGVTlLDQPFDHGdGARSFHLLDPAGNKVQpLYHP 129
Cdd:COG2514   80 AALARLAAAGVP-VEGAVDHG-VGESLYFRDPDGNLIE-LYTD 119

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  11 LNGLRHLALLVPNLEECERFYVDVLGMEVLNRaNEDLVYLTCGNDNLSL----GRAHAASNGLQTMDHYGFVVDSVEELE 86
Cdd:COG2514    1 ITRLGHVTLRVRDLERSAAFYTDVLGLEVVER-EGGRVYLRADGGEHLLvleeAPGAPPRPGAAGLDHVAFRVPSRADLD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489189306  87 AWYRYLKALGVTlLDQPFDHGdGARSFHLLDPAGNKVQpLYHP 129
Cdd:COG2514   80 AALARLAAAGVP-VEGAVDHG-VGESLYFRDPDGNLIE-LYTD 119

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNRA-NEDLVYLTCGND-NLSLGR-AHAASNGLQTMDHYGFVVDSVEELEAWYRYL 92
Cdd:cd06587    1 HVALRVPDLDASVAFYEEVLGFEVVSRNeGGGFAFLRLGPGlRLALLEgPEPERPGGGGLFHLAFEVDDVDEVDERLREA 80

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489189306  93 KALGVTLLDqPFDHGDGARSFHLLDPAGNKV 123
Cdd:cd06587   81 GAEGELVAP-PVDDPWGGRSFYFRDPDGNLI 110

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  11 LNGLRHLALLVPNLEECERFYVDVLGMEVLNRaNEDLVYLTCGNDNLSL----GRAHAASNGLQTMDHYGFVVDSVEELE 86
Cdd:COG2514    1 ITRLGHVTLRVRDLERSAAFYTDVLGLEVVER-EGGRVYLRADGGEHLLvleeAPGAPPRPGAAGLDHVAFRVPSRADLD 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 489189306  87 AWYRYLKALGVTlLDQPFDHGdGARSFHLLDPAGNKVQpLYHP 129
Cdd:COG2514   80 AALARLAAAGVP-VEGAVDHG-VGESLYFRDPDGNLIE-LYTD 119

Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306   16 HLALLVPNLEECERFYVDVLGMEVLNRANED------LVYLTCGNDNLSLGRAHAASN--GLQTMDHYGFVVDSVEELEA 87
Cdd:pfam00903   4 HVALRVGDLEKSLDFYTDVLGFKLVEETDAGeegglrSAFFLAGGRVLELLLNETPPPaaAGFGGHHIAFIAFSVDDVDA 83

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 489189306   88 WYRYLKALGVTLLDQPFDHGDGARSFHLLDPAGNKVQ 124
Cdd:pfam00903  84 AYDRLKAAGVEIVREPGRHGWGGRYSYFRDPDGNLIE 120

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  12 NGLRHLALLVPNLEECERFYVDVLGMEVLNRANEDLVYLTCGNDN-LSLGRAHAASNGLQTMDHYGFVVDSVEeleAWYR 90
Cdd:COG3324    3 GTIVWVELPVDDLERAKAFYEEVFGWTFEDDAGPGGDYAEFDTDGgQVGGLMPGAEEPGGPGWLLYFAVDDLD---AAVA 79

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 489189306  91 YLKALGVTLLDQPFDHGDGARSFHLLDPAGNKVQpLYHPA 130
Cdd:COG3324   80 RVEAAGGTVLRPPTDIPPWGRFAVFRDPEGNRFG-LWQPA 118

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNRaNEDLVYLTCGND---NLSLGRAHAASnglqtMDHYGFVVDSVEELEAWYRYL 92
Cdd:cd16360    1 YAELGVPDLEKALEFYTDVLGLQVAKR-DGNSVYLRGYEDehhSLVLYEAPEAG-----LKHFAFEVASEEDLERAAASL 74

                         90       100       110
                 ....*....|....*....|....*....|.
gi 489189306  93 KALG--VTLLDQPFDHGDGARsFHLLDPAGN 121
Cdd:cd16360   75 TALGcdVTWGPDGEVPGGGKG-FRFQDPSGH 104

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).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  11 LNGLRHLALLVPNLEECERFYVDVLGMEVLnRANEDLVYL-TCGNDNLSLGRAHAASNGLqtmDHYGFVVDSVEELEAWY 89
Cdd:cd08362    1 VTHLRYVALGVPDLAAEREFYTEVWGLEEV-AEDDDVVYLrAEGSEHHVLRLRQSDENRL---DLIAFAAATRADVDALA 76

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489189306  90 RYLKALGVTLLDQPF---DHGDGARsFHLLDPAG 120
Cdd:cd08362   77 ARLAAAGVRILSEPGpldDPGGGYG-FRFFDPDG 109

N-terminal domain of catechol 2,3-dioxygenase; This subfamily contains the N-terminal, non-catalytic, domain of catechol 2,3-dioxygenase. Catechol 2,3-dioxygenase (2,3-CTD, catechol:oxygen 2,3-oxidoreductase) catalyzes an extradiol cleavage of catechol to form 2-hydroxymuconate semialdehyde with the insertion of two atoms of oxygen. The enzyme is a homotetramer and contains catalytically essential Fe(II) . The reaction proceeds by an ordered bi-unit mechanism. First, catechol binds to the enzyme, this is then followed by the binding of dioxygen to form a tertiary complex, and then the aromatic ring is cleaved to produce 2-hydroxymuconate semialdehyde. Catechol 2,3-dioxygenase belongs to the type I extradiol dioxygenase family. The subunit comprises 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. This subfamily represents the N-terminal domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNRANEDLVYLTCGN--DNLSLGRAHAASNGlqtMDHYGFVVDSVEELEAWYRYLK 93
Cdd:cd07265    7 HVQLRVLDLEEAIKHYREVLGLVETGRDDQGRVYLKAWDeyDHHSIILREADTAG---LDFMGFKVLDDADLEQLEARLQ 83

                         90
                 ....*....|
gi 489189306  94 ALGVTLLDQP 103
Cdd:cd07265   84 AYGVTVTRIP 93

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  19 LLVPNLEECERFYVDVLGMEVLNRANEDL-----VYLTCGNDNLSLGRAHAASnGLQTMDHYGFVVdSVEELEAWYRYLK 93
Cdd:COG2764    6 LVVDDAEEALEFYEDVFGFEVVFRMTDPDgkimhAELRIGGSVLMLSDAPPDS-PAAEGNGVSLSL-YVDDVDALFARLV 83

                         90       100
                 ....*....|....*....|....*...
gi 489189306  94 ALGVTLLDQPFDHGDGARSFHLLDPAGN 121
Cdd:COG2764   84 AAGATVVMPLQDTFWGDRFGMVRDPFGV 111

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  19 LLVPNLEECERFYVDVLGMEVLNRANEDL-VYLTCGNDNLSLGRAHA---ASNGLqtmdhyGFVVDsVEELEAWYRYLKA 94
Cdd:cd08349    4 LPVRDIDKTLAFYVDVLGFEVDYERPPPGyAILSRGGVELHLFEHPGldpAGSGV------AAYIR-VEDIDALHAELKA 76

                         90       100       110
                 ....*....|....*....|....*....|....
gi 489189306  95 LGVTLLDQPF-----DHGDGARSFHLLDPAGNKV 123
Cdd:cd08349   77 AGLPLFGIPRitpieDKPWGMREFAVVDPDGNLL 110

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNR----AN---ED----LVYLTCGNDnlslgrahaasnGLQTMDHYGFVVDSVEE 84
Cdd:cd07254    4 HLSLNVTDLERSIRFYSDLFGAEPAKRkadyAKfmlEDpplnLALLVNDRK------------EPYGLNHLGIQVDSKEE 71

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489189306  85 LEAWYRYLKALGVTLLDQPFDHGDGARS--FHLLDPAGN 121
Cdd:cd07254   72 VAALKARAEAAGLPVRKEPRTTCCYAVQdkFWLTDPDGN 110

metallothiol transferase FosB;

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  10 RLNGLRHLALLVPNLEECERFYVDVLGMEVLNRAnEDLVYLTCGNDNLSLG-RAHAASNGL-QTMDHYGFVVDSvEELEA 87
Cdd:PRK04101   1 MLKGINHICFSVSNLEKSIEFYEKVLGAKLLVKG-RKTAYFDLNGLWIALNeEKDIPRNEIhQSYTHIAFSIEE-EDFDH 78

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489189306  88 WYRYLKALGVTLLD-QPFDHGDGaRSFHLLDPAGNK 122
Cdd:PRK04101  79 WYQRLKENDVNILPgRERDERDK-KSIYFTDPDGHK 113

N-terminal domain of MhqB, a type I extradiol dioxygenase, and similar proteins; This subfamily contains the N-terminal, non-catalytic, domain of Burkholderia sp. NF100 MhqB and similar proteins. MhqB is a type I extradiol dioxygenase involved in the catabolism of methylhydroquinone, an intermediate in the degradation of fenitrothion. The purified enzyme has shown extradiol ring cleavage activity toward 3-methylcatechol. Fe2+ was suggested as a cofactor, the same as most other enzymes in the family. Burkholderia sp. NF100 MhqB is encoded on the plasmid pNF1. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  14 LRHLALLVPNLEECERFYvDVLGMEVlNRANEDLVYLTCGNDN----LSLGRAHAASngLQTMDHYGfvvdsvEELEAWY 89
Cdd:cd08344    3 IDHFALEVPDLEVARRFY-EAFGLDV-RETGEDLELRAPGNDHvwarLIQGARKRLA--YLSFGIFG------DDLARFA 72

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489189306  90 RYLKALGVTLLDQPFDHGDGArsFHLLDPAGNKVQ 124
Cdd:cd08344   73 AHLDAAGVALIAAPPGADPDG--VWFEDPDGNLLQ 105

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNRA-NEDLVYLTCGNDN-----LSLGR----AHAASNGLQTmDHYGFVVDSVEEL 85
Cdd:cd07263    1 QVMLYVDDQDKALDFYVEKLGFEVVEDVpMGGMRWVTVAPPGspgtsLLLEPkahpAQMPQSPEAA-GGTPGILLATDDI 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 489189306  86 EAWYRYLKALGVTLLDQPFDHGdGARSFHLLDPAGNKVQ 124
Cdd:cd07263   80 DATYERLTAAGVTFVQEPTQMG-GGRVANFRDPDGNLFA 117

C-terminal domain of type I, class II extradiol dioxygenases, catalytic domain; This family contains the C-terminal, 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGM---EVLNRANED-LVYLTCGN--DNLSLGRAHAASNGLQtmdHYGFVVDSVEELEAWY 89
Cdd:cd08343    2 HVVLCSPDVEASRDFYTDVLGFrvsDRIVDPGVDgGAFLHCDRgtDHHTVALAGGPHPGLH---HVAFEVHDLDDVGRGH 78

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 489189306  90 RYLKALGVTLLDQPFDHGDG-ARSFHLLDPAGNKV 123
Cdd:cd08343   79 DRLREKGYKIEWGPGRHGLGsQVFDYWFDPSGNRV 113

Fosfomycin resistant protein; This family contains three types of fosfomycin resistant protein. Fosfomycin inhibits the enzyme UDP-N-acetylglucosamine-3-enolpyruvyltransferase (MurA), which catalyzes the first committed step in bacterial cell wall biosynthesis. The three types of fosfomycin resistance proteins, employ different mechanisms to render fosfomycin [(1R,2S)-epoxypropylphosphonic acid] inactive. FosB catalyzes the addition of L-cysteine to the epoxide ring of fosfomycin. FosX catalyzes the addition of a water molecule to the C1 position of the antibiotic with inversion of configuration at C1. FosA catalyzes the addition of glutathione to the antibiotic fosfomycin, making it inactive. Catalytic activities of both FosX and FosA are Mn(II)-dependent, but FosB is activated by Mg(II). Fosfomycin resistant proteins are evolutionarily related to glyoxalase I and type I extradiol dioxygenases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLG-MEVLNRANED-----LVYLTCGNDNLSLGRAHAASNglQTMDHYGFVVDSvEELEAWY 89
Cdd:cd08345    1 HITLIVRDLEKSTAFLQDIFGaREVYSSGDKTfslskEKFFLLGGLWIALMEGESLQE--RSYTHIAFQIQS-EDFDRYA 77

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489189306  90 RYLKALGVTLLDQ-PFDHGDGaRSFHLLDPAGNKVQ 124
Cdd:cd08345   78 ERLGALGVEMRPPrPRVEGEG-RSIYFYDPDNHLFE 112

N-terminal domain of 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD); This subfamily contains the N-terminal, non-catalytic, domain of HPCD. HPCD catalyses the second step in the degradation of 4-hydroxyphenylacetate to succinate and pyruvate. The aromatic ring of 4-hydroxyphenylacetate is opened by this dioxygenase to yield the 3,4-diol product, 2-hydroxy-5-carboxymethylmuconate semialdehyde. HPCD is a homotetramer and each monomer contains two structurally homologous barrel-shaped domains at the N- and C-terminus. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism. Most extradiol dioxygenases contain Fe(II) in their active site, but HPCD can be activated by either Mn(II) or Fe(II). These enzymes belong to the type I class II family of extradiol dioxygenases. The class III 3,4-dihydroxyphenylacetate 2,3-dioxygenases belong to a different superfamily.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  14 LRHLALLVPNLEECERFYVDVLGMEVlNRANEDLVYLTCGND----NLSLGRAHAASNGlqtmdHYGFVVDSVEELEAWY 89
Cdd:cd07266    5 LAHAELVVTDLAASREFYVDTLGLHV-TDEDDNAIYLRGVEEfihhTLVLRKAPEAAVG-----HLGFRVRDEADLDKAA 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 489189306  90 RYLKALG--VTLLDQPFDhgdgARSFHLLDPAG 120
Cdd:cd07266   79 AFYKELGlpTEWREEPGQ----GRTLRVEDPFG 107

vicinal oxygen chelate (VOC) family protein Bacillus subtilis YwkD and similar proteins; uncharacterized subfamily of vicinal oxygen chelate (VOC) family contains Bacillus subtilis YwkD 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  12 NGLRHLALLVPNLEECERFYVDVLGMEVLN---RANED--LVYLTCGNDNLSL----------GRAHAAsnGLQtmdHYG 76
Cdd:cd08352    1 KKIHHIAIICSDYEKSKDFYVDKLGFEIIRehyRPERNdiKLDLALGGYQLELfikpdaparpSYPEAL--GLR---HLA 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 489189306  77 FVVDSVeelEAWYRYLKALGVTLLDQPFDHGDGARSFHLLDPAG 120
Cdd:cd08352   76 FKVEDV---EATVAELKSLGIETEPIRVDDFTGKKFTFFFDPDG 116

N-terminal domain of 2,3-dihydroxy-p-cumate-3,4-dioxygenase (PpCmtC); This subfamily contains the N-terminal, non-catalytic, domain of PpCmtC. 2,3-dihydroxy-p-cumate-3,4-dioxygenase (CmtC of Pseudomonas putida F1) is a dioxygenase involved in the eight-step catabolism pathway of p-cymene. CmtC acts upon the reaction intermediate 2,3-dihydroxy-p-cumate, yielding 2-hydroxy-3-carboxy-6-oxo-7-methylocta-2,4-dienoate. The CmtC belongs to the type I family of extradiol dioxygenases. Fe2+ was suggested as a cofactor, same as other enzymes in the family. The type I family of extradiol dioxygenases contains two structurally homologous barrel-shaped domains at the N- and C-terminal. The active-site metal is located in the C-terminal barrel and plays an essential role in the catalytic mechanism.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  14 LRHLALLVPNLEECERFYVDVLGMEVLNRANeDLVYLTcgNDNlslgRAHA-----ASNGLQTMdhyGFVVDSVEELEAW 88
Cdd:cd08361    7 IRYVRLGTRDLEEAVRFATDILGLELVRREG-GAAYFR--SDD----RDHTlcyfeGDPAEQTS---GFEVRDPAELDAA 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 489189306  89 YRYLKALGVtlldqPFDHG--DGARSFH------LLDPAGNKVQPLYHPAVSG 133
Cdd:cd08361   77 AAELESAGI-----AVRRGtaEECEQRRvrafisFRDPSGNRIELVVRPHHSG 124

uncharacterized subfamily of vicinal oxygen chelate (VOC) familyprotein, glyoxalase I, and type I ring-cleaving dioxygenases; 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEvLNRANEDLVYLTCGNDNLSlgrAHAASNGLQT-----------MDHYGFVVDsVEE 84
Cdd:cd08357    2 HLAIPVRDLEAARDFYGDVLGCP-EGRSSETWIDFNFFGHQVV---AHLVPNYASTstnavdghsvpVPHFGLALT-VDD 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 489189306  85 LEAWYRYLKALGVTLLDQPFDHGDGA----RSFHLLDPAGN 121
Cdd:cd08357   77 FDALAERLKAAGVKFYIEPYVRFEGEpgeqWTMFLLDPSGN 117

C-terminal domain of 2,3-dihydroxybiphenyl 1,2-dioxygenase; This subfamily contains the C-terminal, catalytic, domain of BphC1-RGP6 and similar proteins. BphC catalyzes the extradiol ring cleavage reaction of 2,3-dihydroxybiphenyl, the third step in the polychlorinated biphenyls (PCBs) degradation pathway (bph pathway). This subfamily of BphCs belongs to the type I extradiol dioxygenase family, which require a metal in the active site in its catalytic mechanism. Polychlorinated biphenyl degrading bacteria demonstrate a multiplicity of BphCs. For example, three types of BphC enzymes have been found in Rhodococcus globerulus (BphC1-RGP6 - BphC3-RGP6), all three enzymes are type I extradiol dioxygenases. BphC1-RGP6 has an internal duplication, it is a two-domain dioxygenase which forms octamers, and has Fe(II) at the catalytic site. Its C-terminal repeat is represented in this subfamily. BphC2-RGP6 and BphC3-RGP6 are one-domain dioxygenases, they belong to a different subfamily of the ED_TypeI_classII_C (C-terminal domain of type I, class II extradiol dioxygenases) family.

                         10        20
                 ....*....|....*....|....*.
gi 489189306  13 GLRHLALLVPNLEECERFYVDVLGME 38
Cdd:cd07237    9 GLGHVVLIVPDVDEALAFYTDVLGFR 34

C-terminal of Bacillus subtilis CatE like protein, a vicinal oxygen chelate subfamily; Uncharacterized subfamily of vicinal oxygen chelate (VOC) superfamily contains Bacillus subtilis CatE and similar proteins. CatE is proposed to function as Catechol-2,3-dioxygenase. VOC 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  16 HLALLVPNLEECERFYVDVLGMEVLNRANeDLVYLTCGNDNLSLG-----RAHAASNGLQT--MDHYGFVVDSVEELEAW 88
Cdd:cd16359    2 HIHLRVSDLKAASHFYHQVLGFDIKSRRP-GALFLSAGGYHHHIGlntwaGRGLPLPPEDAtgLAYFTIVLPDQEALAAI 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 489189306  89 YRYLKALGVTLLDQPfdhgdgaRSFHLLDPAGNKVQ 124
Cdd:cd16359   81 LERLDLAGYDVEALD-------DGLELTDPWGITVK 109

N-terminal domain of Streptomyces griseus SgaA and similar domains; SgaA suppresses the growth disturbances caused by high osmolarity and a high concentration of A-factor, a microbial hormone, during the early growth phase in Streptomyces griseus. A-factor (2-isocapryloyl-3R-hydroxymethyl-gamma-butyrolactone) controls morphological differentiation and secondary metabolism in Streptomyces griseus. It is a chemical signaling molecule that at a very low concentration acts as a switch for yellow pigment production, aerial mycelium formation, streptomycin production, and streptomycin resistance. The structure and amino acid sequence of SgaA are closely related to a group of antibiotics resistance proteins, including bleomycin resistance protein, mitomycin resistance protein, and fosfomycin resistance proteins. SgaA might also function as a streptomycin resistance protein.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489189306  19 LLVPNLEECERFYVDVLG--MEVLNRANEDLVYLTC-GNDNLSLGRAHAASNGLQTMDHYGFVVDSVEE-LEAwyryLKA 94
Cdd:cd07247    6 LPTTDLERAKAFYGAVFGwtFEDEGDGGGDYALFTAgGGAVGGLMRAPEEVAGAPPGWLIYFAVDDLDAaLAR----VEA 81

                         90       100
                 ....*....|....*....|....*..
gi 489189306  95 LGVTLLDQPFDHGDGARSFHLLDPAGN 121
Cdd:cd07247   82 AGGKVVVPPTDIPGGGRFAVFADPEGN 108

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.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489189306  77 FVVDSVEELEAWYRYLKALGVTLLDQPFDHGDGARSFHLLDPAGN 121
Cdd:cd16356   71 FDVDDVEAVDRLVPRAAALGATLIKPPYDTYYGWYQAVLLDPEGN 115