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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465   3 RIYACPVADVPEGEALRIDTS-PVIALFNVGGEFYAINDRCSHGNASMSEGYLEDDaTVECPLHAASFCLKTGKALCLPA 81
Cdd:cd03528   1 WVRVCAVDELPEGEPKRVDVGgRPIAVYRVDGEFYATDDLCTHGDASLSEGYVEGG-VIECPLHGGRFDLRTGKALSLPA 79

                        90
                ....*....|....*....
gi 16130465  82 TDPLTTYPVHVEGGDIFID 100
Cdd:cd03528  80 TEPLKTYPVKVEDGDVYVD 98

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 16130465     2 NRIYACPVADVPEGEALRIDTSPV-IALFNV-GGEFYAINDRCSHGNASMSEGYLEDDATVECPLHAASFCLkTGKALCL 79
Cdd:pfam00355   1 SWYPVCHSSELPEGEPKVVEVGGEpLVVFRDeDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDG-TGKVVKV 79

                          90
                  ....*....|
gi 16130465    80 PATDPLTTYP 89
Cdd:pfam00355  80 PAPRPLKSYP 89

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465   3 RIYACPVADVPEGEALRIDTS-PVIALFNVGGEFYAINDRCSHGNASMSEGYLEDDaTVECPLHAASFCLKTGKALCLPA 81
Cdd:cd03528   1 WVRVCAVDELPEGEPKRVDVGgRPIAVYRVDGEFYATDDLCTHGDASLSEGYVEGG-VIECPLHGGRFDLRTGKALSLPA 79

                        90
                ....*....|....*....
gi 16130465  82 TDPLTTYPVHVEGGDIFID 100
Cdd:cd03528  80 TEPLKTYPVKVEDGDVYVD 98

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 16130465     2 NRIYACPVADVPEGEALRIDTSPV-IALFNV-GGEFYAINDRCSHGNASMSEGYLEDDATVECPLHAASFCLkTGKALCL 79
Cdd:pfam00355   1 SWYPVCHSSELPEGEPKVVEVGGEpLVVFRDeDGELYALEDRCPHRGAPLSEGKVNGGGRLECPYHGWRFDG-TGKVVKV 79

                          90
                  ....*....|
gi 16130465    80 PATDPLTTYP 89
Cdd:pfam00355  80 PAPRPLKSYP 89

Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465   3 RIYACPVADVPEGEA--LRIDTSPVIALFNVGGEFYAINDRCSHGNASMSEGYLEDDaTVECPLHAASFCLKTGKALCLP 80
Cdd:cd03467   1 WVVVGALSELPPGGGrvVVVGGGPVVVVRREGGEVYALSNRCTHQGCPLSEGEGEDG-CIVCPCHGSRFDLRTGEVVSGP 79

                        90
                ....*....|....*....
gi 16130465  81 ATDPLTTYPVHVEGGDIFI 99
Cdd:cd03467  80 APRPLPKYPVKVEGDGVVW 98

Rieske [2Fe-2S] domain protein, MocE subfamily; This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465     2 NRIYACPVADVPEGEALRIDTS-PVIALF-NVGGEFYAINDRCSHGNASMSEGYLEDDaTVECPLHAASFCLKTGKALCL 79
Cdd:TIGR02377   1 NWVKACDADDIGREDVARFDHGgRTFAIYrTPDDQYYATDGLCTHEYAHLADGLVMDT-TVECPKHAGCFDYRTGEALNP 79

                          90       100
                  ....*....|....*....|..
gi 16130465    80 PATDPLTTYPVHVEGGDIFIDL 101
Cdd:TIGR02377  80 PVCVNLKTYPVKVVDGAVYVDI 101

Toluene-4-monooxygenase effector protein complex (T4mo), Rieske ferredoxin subunit; The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. T4mo is a four-protein complex that catalyzes the NADH- and O2-dependent hydroxylation of toluene to form p-cresol. T4mo consists of an NADH oxidoreductase (T4moF), a diiron hydroxylase (T4moH), a catalytic effector protein (T4moD), and a Rieske ferredoxin (T4moC). T4moC contains a Rieske domain and functions as an obligate electron carrier between T4moF and T4moH. 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465   3 RIYACPVADVPEGEALRIDTS--PVIALFNVGGEFYAINDRCSHGNASMSEGYlEDDATVECPLHAASFCLKTGKALClP 80
Cdd:cd03474   1 FTKVCSLDDVWEGEMELVDVDgeEVLLVAPEGGEFRAFQGICPHQEIPLAEGG-FDGGVLTCRAHLWQFDADTGEGLN-P 78

                        90       100
                ....*....|....*....|....*.
gi 16130465  81 ATDPLTTYPVHVEGGDIFIDLPEAQP 106
Cdd:cd03474  79 RDCRLARYPVKVEGGDILVDTEGVLP 104

Rieske-like [2Fe-2S] domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465     7 CPVADVPE--GEALRIDTSPViALFNV-GGEFYAINDRCSHGNAS-MSEGYLED---DATVECPLHAASFCLKTGKalCL 79
Cdd:pfam13806   5 CALDDLPPgtGVCALVGGRQV-AVFRLeDGQVYAIDNRDPFSGANvLSRGIVGDlggELVVASPLYKQHFDLKTGE--CL 81

                          90       100
                  ....*....|....*....|..
gi 16130465    80 PATD-PLTTYPVHVEGGDIFID 100
Cdd:pfam13806  82 EDPEvSVPVYPVRVRDGNVEVQ 103

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 16130465  10 ADVPEGE--ALRIDTSPVIaLFNVGGEFYAINDRCSHGNASMSEG-YLEDDATVECPLHAASFCLKTGKaLCLPATDP-- 84
Cdd:cd03548  22 HELEEGEpkGIQLCGEPIL-LRRVDGKVYALKDRCLHRGVPLSKKpECFTKGTITCWYHGWTYRLDDGK-LVTILANPdd 99

                        90       100
                ....*....|....*....|..
gi 16130465  85 -------LTTYPVHVEGGDIFI 99
Cdd:cd03548 100 pligrtgLKTYPVEEAKGMIFV 121

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).

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16130465  26 IALFNVG-GEFYAINDRCSHGNASMSEGYLEDDATVeCPLHAASF-----CLKTGKALCLPATDPLTTYPVHVEGGDIFI 99
Cdd:cd03532  29 VVLYRTQdGRVAALEDRCPHRSAPLSKGSVEGGGLV-CGYHGLEFdsdgrCVHMPGQERVPAKACVRSYPVVERDALIWI 107

pheophorbide a oxygenase

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 16130465   33 GEFYAINDRCSHGNASMSEGYLEDDATVECPLHAASF 69
Cdd:PLN02518 124 GEWVAFDDKCPHRLAPLSEGRIDENGHLQCSYHGWSF 160