C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of anthranilate 1,2-dioxygenase (AntDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and the C-terminal catalytic domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this subgroup include the alpha subunits of AntDO, aniline dioxygenase, Acinetobacter calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS, 2,4,5-trichlorophenoxyacetic acid oxygenase from Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic acid oxygenase from Bradyrhizobium sp. strain HW13, p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase form Pseudomonas cepacia 2CBS, and Pseudomonas putida IacC, which may be involved in the catabolism of the plant hormone indole 3-acetic acid. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 198 GKSSYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNASKGeeldtLDYSKLGagdsETDDGWFSFKNGHSVLFS 277
Cdd:cd08879    2 GTHRYRYRGNWKLQLENGTDGYHPPFVHASYVATTGAAAADATRGG-----LSSFMTG----PQGGGVRDLGNGHSVLDS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 278 DMPNP-----TVRPGYSTVMPYMVEKYGDKYAEWAM-HRLRNLNLYPSLFFMDQiSSQLRIVRPVAWNKTEVISQCIGVK 351
Cdd:cd08879   73 RPEIPrldadRPKPPIAEYRAALVAAHGEERARRILrGRGRNLNIFPNLFIIDI-SQQIRVIRPIAVDETEVTSWALRPK 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 352 GESAEARRNRIRQFEDFFNVSGLGTPDDLVEFREQQKGFQARLERWSDISRGCQSWEYGatknsqDLGIQPVITgrefTH 431
Cdd:cd08879  152 GAPDEVNRRRLRYSEDFFGPSGFATPDDLEAFERCQRGLAARGEEWVDLSRGLGREKAD------EDGVVTGAV----TD 221

                        250
                 ....*....|....*.
gi 488042308 432 EGLYVNQHGHWQRLML 447
Cdd:cd08879  222 ELPMRNQWRAWKRLMT 237

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308   51 WIYACHESEIPNNHDFlTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSTFTCPFHAWCYKSDGRLVKVK 130
Cdd:pfam00355   2 WYPVCHSSELPEGEPK-VVEVGGEPLVVFRDEDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDGTGKVVKVP 80

                  ....
gi 488042308  131 APSE 134
Cdd:pfam00355  81 APRP 84

C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase and related aromatic ring hydroxylating dioxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of anthranilate 1,2-dioxygenase (AntDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). RHOs utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and the C-terminal catalytic domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this subgroup include the alpha subunits of AntDO, aniline dioxygenase, Acinetobacter calcoaceticus benzoate 1,2-dioxygenase, 2-halobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS, 2,4,5-trichlorophenoxyacetic acid oxygenase from Pseudomonas cepacia AC1100, 2,4-dichlorophenoxyacetic acid oxygenase from Bradyrhizobium sp. strain HW13, p-cumate 2,3-dioxygenase, 2-halobenzoate 1,2-dioxygenase form Pseudomonas cepacia 2CBS, and Pseudomonas putida IacC, which may be involved in the catabolism of the plant hormone indole 3-acetic acid. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 198 GKSSYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNASKGeeldtLDYSKLGagdsETDDGWFSFKNGHSVLFS 277
Cdd:cd08879    2 GTHRYRYRGNWKLQLENGTDGYHPPFVHASYVATTGAAAADATRGG-----LSSFMTG----PQGGGVRDLGNGHSVLDS 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 278 DMPNP-----TVRPGYSTVMPYMVEKYGDKYAEWAM-HRLRNLNLYPSLFFMDQiSSQLRIVRPVAWNKTEVISQCIGVK 351
Cdd:cd08879   73 RPEIPrldadRPKPPIAEYRAALVAAHGEERARRILrGRGRNLNIFPNLFIIDI-SQQIRVIRPIAVDETEVTSWALRPK 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 352 GESAEARRNRIRQFEDFFNVSGLGTPDDLVEFREQQKGFQARLERWSDISRGCQSWEYGatknsqDLGIQPVITgrefTH 431
Cdd:cd08879  152 GAPDEVNRRRLRYSEDFFGPSGFATPDDLEAFERCQRGLAARGEEWVDLSRGLGREKAD------EDGVVTGAV----TD 221

                        250
                 ....*....|....*.
gi 488042308 432 EGLYVNQHGHWQRLML 447
Cdd:cd08879  222 ELPMRNQWRAWKRLMT 237

Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the initial source of two electrons for dioxygen activation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  51 WIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSTFTCPFHAWCYKSDGRLVKVK 130
Cdd:cd03469    1 WYFVGHSSELPEPGDYVTLELGGEPLVLVRDRDGEVRAFHNVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLDGKLVGVP 80

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 488042308 131 APSEYcEDFDKSSRGLKQGRIASYRGFVFVSLDTQA 166
Cdd:cd03469   81 REEGF-PGFDKEKLGLRTVPVEEWGGLIFVNLDPDA 115

Rieske non-heme iron oxygenase (RO) family, Ortho-halobenzoate-1,2-dioxygenase (OHBDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of OHBDO, salicylate 5-hydroxylase (S5H), terephthalate 1,2-dioxygenase system (TERDOS) and similar proteins. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OHBDO converts 2-chlorobenzoate (2-CBA) to catechol as well as 2,4-dCBA and 2,5-dCBA to 4-chlorocatechol, as part of the chlorobenzoate degradation pathway. Although ortho-substituted chlorobenzoates appear to be particularly recalcitrant to biodegradation, several strains utilize 2-CBA and the dCBA derivatives as a sole carbon and energy source. S5H converts salicylate (2-hydroxybenzoate), a metabolic intermediate of phenanthrene, to gentisate (2,5-dihydroxybenzoate) as part of an alternate pathway for naphthalene catabolism. S5H is a multicomponent enzyme made up of NagGH (the oxygenase components), NagAa (the ferredoxin reductase component), and NagAb (the ferredoxin component). The oxygenase component is made up of alpha (NagG) and beta (NagH) subunits. TERDOS is present in gram-positive bacteria and proteobacteria where it converts terephthalate (1,4-dicarboxybenzene) to protocatechuate as part of the terephthalate degradation pathway. The oxygenase component of TERDOS, called TerZ, is a hetero-hexamer with 3 alpha (TerZalpha) and 3 beta (TerZbeta) subunits.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  27 RIARNMFTEPELFDLEMELIFE-KVWIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAK 105
Cdd:cd03545    1 RVPYKVFTDRAYFDREQERIFRgKTWSYVGLEAEIPNAGDFKSTFVGDTPVVVTRAEDGSLHAWVNRCAHRGALVCRERR 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488042308 106 GNQSTFTCPFHAWCYKSDGRLVKV------KAPSEYCEDFDKSSRGLKQGRIASYRGFVFVSLD 163
Cdd:cd03545   81 GNDGSLTCVYHQWAYDLKGNLKGVpfrrglKGQGGMPKDFDMKQHGLEKLRVETVGGLVFASFS 144

Rieske non-heme iron oxygenase (RO) family, Nathphalene 1,2-dioxygenase (NDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. NDO is a three-component RO system consisting of a reductase, a ferredoxin, and a hetero-hexameric alpha-beta subunit oxygenase component. NDO catalyzes the oxidation of naphthalene to cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene (naphthalene cis-dihydrodiol) with the consumption of O2 and NAD(P)H. NDO has a relaxed substrate specificity and can oxidize almost 100 substrates. Included in its varied activities are the enantiospecific cis-dihydroxylation of polycyclic aromatic hydrocarbons and benzocycloalkenes, benzylic hydroxylation, N- and O-dealkylation, sulfoxidation and desaturation reactions.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  49 KVWIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSTFTCPFHAWCYKSDGRLVK 128
Cdd:cd03535    1 RAWVFLGHESEIPNAGDYVVRYIGDDSFIVCRDEDGEIRAMFNSCRHRGMQVCRAEMGNTSHFRCPYHGWTYRNTGRLVG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 488042308 129 VKAPSE-YCEDFDKSSRGLKQG-RIASYRGFVFVSLDTQA 166
Cdd:cd03535   81 VPAQQEaYGGGFDKSQWGLRPApNLDSYNGLIFGSLDPKA 120

Rieske [2Fe-2S] domain; The rieske domain has a [2Fe-2S] centre. Two conserved cysteines coordinate one Fe ion, while the other Fe ion is coordinated by two conserved histidines. In hyperthermophilic archaea there is a SKTPCX(2-3)C motif at the C-terminus. The cysteines in this motif form a disulphide bridge, which stabilizes the protein.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308   51 WIYACHESEIPNNHDFlTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSTFTCPFHAWCYKSDGRLVKVK 130
Cdd:pfam00355   2 WYPVCHSSELPEGEPK-VVEVGGEPLVVFRDEDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDGTGKVVKVP 80

                  ....
gi 488042308  131 APSE 134
Cdd:pfam00355  81 APRP 84

This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit (DitA) of diterpenoid dioxygenase (DTDO). DTDO is a novel aromatic-ring-hydroxylating dioxygenase found in Pseudomonas and other proteobacteria that degrades dehydroabietic acid (DhA). Specifically, DitA hydroxylates 7-oxodehydroabietic acid to 7-oxo-11,12-dihydroxy-8, 13-abietadien acid. The ditA1 and ditA2 genes encode the alpha and beta subunits of the oxygenase component of DTDO while the ditA3 gene encodes the ferredoxin component of DTDO. The organization of the genes encoding the various diterpenoid dioxygenase components, the phylogenetic distinctiveness of both the alpha subunit and the ferredoxin component, and the unusual iron-sulfur cluster of the ferredoxin all suggest that this enzyme belongs to a new class of aromatic ring-hydroxylating dioxygenases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  51 WIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTRVAKGNQSTFTCPFHAWCYKSDGRLVKVK 130
Cdd:cd03536    1 WVLLGHESEIPNKGDFMVRDMGSDSVIVARDKDGEIHVSLNVCPHRGMRISTTDGGNTQIHVCIYHGWAFRPNGDFIGAP 80

                         90       100       110
                 ....*....|....*....|....*....|...
gi 488042308 131 APSE--YCEDFDKSSRGLKQGRIASYRGFVFVS 161
Cdd:cd03536   81 VEKEcmHGKMRTKAELGLHKARVTLYGGLIFAT 113

C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC), and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. Oxygenases belonging to this family include the alpha subunits of Pseudomonas resinovorans strain CA10 anthranilate 1,2-dioxygenase, Stenotrophomonas maltophilia dicamba O-demethylase, Ralstonia sp. U2 salicylate-5-hydroxylase, Cycloclasticus sp. strain A5 polycyclic aromatic hydrocarbon dioxygenase, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, plant choline monooxygenase, and the polycyclic aromatic hydrocarbon (PAH)-degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. This group also includes the C-terminal catalytic domains of MupW, part of the mupirocin biosynthetic gene cluster in Pseudomonas fluorescens, and Pseudomonas aeruginosa GbcA (glycine betaine catabolism A). This family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 198 GKSSYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQHRQQVNaskgeeldtldysklgaGDSETDDGWFSF-KNGHSVLF 276
Cdd:cd00680    1 GRYEYEVDCNWKLAVENFLECYHVPTVHPDTLATGLPLPLLF-----------------GDHYRVDDTGEGpGEGLSRHW 63

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 277 SDMPNPTVRPGYstvmpymvekygdkyaeWAMHRLRNLNLYPSLFFMDQISS-QLRIVRPVAWNKTEVISQCIGVKGESa 355
Cdd:cd00680   64 GDGKGPQSALPG-----------------LKPGGYLYLYLFPNLMIGLYPDSlQVQQFVPIGPNKTRLEVRLYRPKDED- 125

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 488042308 356 eARRNRIRQFEDFFNVSGLGTPDDLVEFREQQKGFQARLERWSDISR 402
Cdd:cd00680  126 -AREEFDAELESLAGILRQVLDEDIELCERIQRGLRSGAFRGGPLSP 171

Chlorophyllide a oxygenase/letal leaf spot protein [Coenzyme transport and metabolism];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  32 MFTEPELFDLEMELIFEKVWIYACHESEIPNNhDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLT--RVAKGNqs 109
Cdd:COG5749    1 MSSTRQGPGFNQPFIFRNHWYPVAPSEDLKPN-KPKPVTLLGEPLVIWRDSDGKVVALEDRCPHRGAPLSegRVEGGN-- 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 110 tFTCPFHAWCYKSDGRLVKVkaPSEycedfDKSSRGLKQGRIASY-----RGFVFVsldtqaidsledFLGDAKLfldlm 184
Cdd:COG5749   78 -LRCPYHGWQFDGDGKCVHI--PQL-----PENQPIPKNAKVKSYpvqerYGLIWV------------WLGDPPQ----- 132

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 488042308 185 VNQSPTGELEVLQGK------SSYTFAGNWKLQNENGLDGYHVSTVHYNYV 229
Cdd:COG5749  133 ADETPIPDIPELDDPewvatsSVRDLECHYSRLIENLIDPSHVPFVHHGTQ 183

Rieske non-heme iron oxygenase (RO) family, 2-Oxoquinoline 8-monooxygenase (OMO) and Carbazole 1,9a-dioxygenase (CARDO) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. OMO catalyzes the NADH-dependent oxidation of the N-heterocyclic aromatic compound 2-oxoquinoline to 8-hydroxy-2-oxoquinoline, the second step in the bacterial degradation of quinoline. OMO consists of a reductase component (OMR) and an oxygenase component (OMO) that together function to shuttle electrons from the reduced pyridine nucleotide to the active site of OMO, where O2 activation and 2-oxoquinoline hydroxylation occurs. CARDO, which contains oxygenase (CARDO-O), ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R) components, catalyzes the dihydroxylation at the C1 and C9a positions of carbazole. The oxygenase component of OMO and CARDO contain only alpha subunits arranged in a trimeric structure.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  41 LEMELIFEKVWIYACHESEIPNNhDFLTVQIGRQPIIVSRDGkGELHAMVNACEHRGATLT-RVAKGNQSTFTCPFHAWC 119
Cdd:cd03548    5 IDAKWGFRNHWYPALFSHELEEG-EPKGIQLCGEPILLRRVD-GKVYALKDRCLHRGVPLSkKPECFTKGTITCWYHGWT 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308 120 YK-SDGRLVK-VKAPseycEDFDKSSRGLKQGRIASYRGFVFVsldtqaidsledFLGDA 177
Cdd:cd03548   83 YRlDDGKLVTiLANP----DDPLIGRTGLKTYPVEEAKGMIFV------------FVGDG 126

This alignment model represents the N-terminal rieske domain of the oxygenase alpha subunit of aminopyrrolnitrin oxygenase (PrnD). PrnD is a novel Rieske N-oxygenase that catalyzes the final step in the pyrrolnitrin biosynthetic pathway, the oxidation of the amino group in aminopyrrolnitrin to a nitro group, forming the antibiotic pyrrolnitrin. The biosynthesis of pyrrolnitrin is one of the best examples of enzyme-catalyzed arylamine oxidation. Although arylamine oxygenases are widely distributed within the microbial world and used in a variety of metabolic reactions, PrnD represents one of only two known examples of arylamine oxygenases or N-oxygenases involved in arylnitro group formation, the other being AurF involved in aureothin biosynthesis.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  74 QPIIVSRDGKGELHAMVNACEHRGATLT--RVAKGnqsTFTCPFHAWCYKSDGRLVKVKAPSEYCEDFDKSSRGLKQGR- 150
Cdd:cd03537   25 RPCVAWRGATGRAVVMDRHCSHLGANLAdgRVKDG---CIQCPFHHWRYDEQGQCVHIPGHSTAVRRLEPVPRGARQPTl 101

                         90
                 ....*....|.
gi 488042308 151 -IASYRGFVFV 160
Cdd:cd03537  102 vTAERYGYVWV 112

Rieske non-heme iron oxygenase (RO) family, Phthalate 4,5-dioxygenase (PhDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of PhDO and similar proteins including 3-chlorobenzoate 3,4-dioxygenase (CBDO), phenoxybenzoate dioxygenase (POB-dioxygenase) and 3-nitrobenzoate oxygenase (MnbA). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. PhDO and CBDO are two-component RO systems, containing oxygenase and reductase components. PhDO catalyzes the dihydroxylation of phthalate to form the 4,5-dihydro-cis-dihydrodiol of phthalate (DHD). CBDO, together with CbaC dehydrogenase, converts the environmental pollutant 3CBA to protocatechuate (PCA) and 5-Cl-PCA, which are then metabolized by the chromosomal PCA meta (extradiol) ring fission pathway. POB-dioxygenase catalyzes the initial catabolic step in the angular dioxygenation of phenoxybenzoate, converting mono- and dichlorinated phenoxybenzoates to protocatechuate and chlorophenols. These phenoxybenzoates are metabolic products formed during the degradation of pyrethroid insecticides.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488042308  51 WIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLtRVAKGNQSTFTCPFHAWCYKSDGRLvkVK 130
Cdd:cd03479   22 WQPVALSSELTEDGQPVRVRLLGEDLVAFRDTSGRVGLLDEHCPHRGASL-VFGRVEECGLRCCYHGWKFDVDGQC--LE 98

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 488042308 131 APSEYcedfdKSSRGLKQGRIASY-----RGFVFV 160
Cdd:cd03479   99 MPSEP-----PDSQLKQKVRQPAYpvrerGGLVWA 128

Cao (chlorophyll a oxygenase) is a rieske non-heme iron-sulfur protein located within the plastid-envelope inner and thylakoid membranes, that catalyzes the conversion of chlorophyllide a to chlorophyllide b. CAO is found not only in plants but also in chlorophytes and prochlorophytes. This domain represents the N-terminal rieske domain of the oxygenase alpha subunit. ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Cao is closely related to several other plant RO's including Tic 55, a 55 kDa protein associated with protein transport through the inner chloroplast membrane; Ptc 52, a novel 52 kDa protein isolated from chloroplasts; and LLS1/Pao (Lethal-leaf spot 1/pheophorbide a oxygenase).

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gi 488042308  74 QPIIVSRDGKGELHAMVNACEHRGATLTrVAKGNQSTFTCPFHAWCYKSDGRLVKVkaPSEYC 136
Cdd:cd04337   40 QPWVLFRDEDGTPGCIRDECAHRACPLS-LGKVIEGRIQCPYHGWEYDGDGECTKM--PSTKC 99

Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the insertions that give other Rieske proteins unique structural features are missing. CARDO catalyzes dihydroxylation at the C1 and C9a positions of carbazole. Rieske ferredoxins are found as subunits of membrane oxidase complexes, cis-dihydrodiol-forming aromatic dioxygenases, bacterial assimilatory nitrite reductases, and arsenite oxidase. Rieske ferredoxins are also found as soluble electron carriers in bacterial dioxygenase and monooxygenase complexes.

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gi 488042308  51 WIYACHESEIPNNhDFLTVQIGRQPIIVSRDGkGELHAMVNACEHRGATLTrvaKGNQS--TFTCPFH 116
Cdd:cd03528    1 WVRVCAVDELPEG-EPKRVDVGGRPIAVYRVD-GEFYATDDLCTHGDASLS---EGYVEggVIECPLH 63

Rieske non-heme iron oxygenase (RO) family, Vanillate-O-demethylase oxygenase (VanA) and dicamba O-demethylase oxygenase (DdmC) subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Vanillate-O-demethylase is a heterodimeric enzyme consisting of a terminal oxygenase (VanA) and reductase (VanB) components. This enzyme reductively catalyzes the conversion of vanillate into protocatechuate and formaldehyde. Protocatechuate and vanillate are important intermediate metabolites in the degradation pathway of lignin-derived compounds such as ferulic acid and vanillin by soil microbes. DDmC is the oxygenase component of a three-component dicamba O-demethylase found in Pseudomonas maltophila, that catalyzes the conversion of a widely used herbicide called herbicide dicamba (2-methoxy-3,6-dichlorobenzoic acid) to DCSA (3,6-dichlorosalicylic acid).

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gi 488042308  74 QPIIVSRDGKGELHAMVNACEHRGATLTR---VAKGNQstftCPFHAWCYKSDGRLVKVKAPS 133
Cdd:cd03532   27 EPVVLYRTQDGRVAALEDRCPHRSAPLSKgsvEGGGLV----CGYHGLEFDSDGRCVHMPGQE 85

C-terminal catalytic domain of the oxygenase alpha subunit of an uncharacterized subgroup of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of a functionally uncharacterized subgroup of the Rieske-type non-heme iron aromatic ring-hydroxylating oxygenase (RHO) family. RHOs, also known as aromatic ring hydroxylating dioxygenases, utilize non-heme Fe(II) to catalyze the addition of hydroxyl groups to the aromatic ring, an initial step in the oxidative degradation of aromatic compounds. RHOs are composed of either two or three protein components, and are comprised of an electron transport chain (ETC) and an oxygenase. The ETC transfers reducing equivalents from the electron donor to the oxygenase component, which in turn transfers electrons to the oxygen molecules. The oxygenase components are oligomers, either (alpha)n or (alpha)n(beta)n. The alpha subunits are the catalytic components and have an N-terminal domain, which binds a Rieske-like 2Fe-2S cluster, and a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. This group contains a putative Parvibaculum lavamentivorans (T) DS-1 oxygenase; this organism catabolizes commercial linear alkylbenzenesulfonate surfactant (LAS) and other surfactants, by a pathway involving an undefined 'omega-oxygenation' and beta-oxidation of the LAS side chain. The nature of the LAS-oxygenase is unknown but is likely a multicomponent system. This subfamily belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket.

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gi 488042308 199 KSSYTFAGNWKLQNENGLDGYHVSTVHYNYVSTVQH 234
Cdd:cd08887    3 SRRFDVAANWKLALDGFLEGYHFKVLHKNTIAPYFY 38

chlorophyllide a oxygenase; Provisional

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gi 488042308  51 WIYACHESEIPNNHDFLTVQIGRQPIIVSRDGKGELHAMVNACEHRGATLTrVAKGNQSTFTCPFHAWCYKSDGRLVKVk 130
Cdd:PLN00095  73 WFPVAFAAGLRDEDALIAFDLFNVPWVLFRDADGEAGCIKDECAHRACPLS-LGKLVDGKAQCPYHGWEYETGGECAKM- 150

                         90       100       110
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gi 488042308 131 aPSeyCEDFDKSSRgLKQGRIASYRGFVFV 160
Cdd:PLN00095 151 -PS--CKKFLKGVF-ADAAPVIERDGFIFL 176