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 1966960394  26 WFALCFSRELKR-GAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHGGTVDGEQIVCPFHHYAYGPDGRRIAAR 104
Cdd:cd03469     1 WYFVGHSSELPEpGDYVTLELGGEPLVLVRDRDGEVRAFHNVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLDGKLVGVP 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1966960394 105 CAKGGPALT-----LRTWHVREWNGFVFVWQNADGLAP 137
Cdd:cd03469    81 REEGFPGFDkeklgLRTVPVEEWGGLIFVNLDPDAPPL 118

chlorophyllide a oxygenase; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1966960394   6 RAMHAVGPIDETAPLPYPDGWFALCFSRELKRGAVLTaPFMGRDV--VLYRTASGVACAVDAYCPHQGAHLGHGGTVDGe 83
Cdd:PLN00095   53 RARGAPGVDGAGATADARAHWFPVAFAAGLRDEDALI-AFDLFNVpwVLFRDADGEAGCIKDECAHRACPLSLGKLVDG- 130

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1966960394  84 QIVCPFHHYAYGPDGRRIA-ARCAKGGPALTLRTWHVREWNGFVFVW 129
Cdd:PLN00095  131 KAQCPYHGWEYETGGECAKmPSCKKFLKGVFADAAPVIERDGFIFLW 177

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 1966960394  26 WFALCFSRELKR-GAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHGGTVDGEQIVCPFHHYAYGPDGRRIAAR 104
Cdd:cd03469     1 WYFVGHSSELPEpGDYVTLELGGEPLVLVRDRDGEVRAFHNVCPHRGARLCEGRGGNAGRLVCPYHGWTYDLDGKLVGVP 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1966960394 105 CAKGGPALT-----LRTWHVREWNGFVFVWQNADGLAP 137
Cdd:cd03469    81 REEGFPGFDkeklgLRTVPVEEWGGLIFVNLDPDAPPL 118

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 1966960394  24 DGWFALCFSRELKRGaVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHgGTVDGEQIVCPFHHYAYGPDGRRIAA 103
Cdd:cd03532     4 NAWYVAAWADELGDK-PLARTLLGEPVVLYRTQDGRVAALEDRCPHRSAPLSK-GSVEGGGLVCGYHGLEFDSDGRCVHM 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1966960394 104 RCAKGGPA-LTLRTWHVREWNGFVFVWQNADGLA 136
Cdd:cd03532    82 PGQERVPAkACVRSYPVVERDALIWIWMGDAALA 115

Ferredoxin subunit of nitrite reductase or a ring-hydroxylating dioxygenase [Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1966960394  26 WFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVaCAVDAYCPHQGAHLgHGGTVDGEQIVCPFHHYAYGP-DGRRIAAR 104
Cdd:COG2146     3 EVKVCALDDLPEGGGVVVEVGGKQIAVFRTDGEV-YAYDNRCPHQGAPL-SEGIVDGGVVTCPLHGARFDLrTGECLGGP 80

                          90       100
                  ....*....|....*....|....
gi 1966960394 105 CAKGgpaltLRTWHVREWNGFVFV 128
Cdd:COG2146    81 ATEP-----LKTYPVRVEDGDVYV 99

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 1966960394  26 WFALCFSRELKR-GAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHgGTVDGEQIVCPFHHYAYGPDGRRIAAR 104
Cdd:cd03479    22 WQPVALSSELTEdGQPVRVRLLGEDLVAFRDTSGRVGLLDEHCPHRGASLVF-GRVEECGLRCCYHGWKFDVDGQCLEMP 100

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1966960394 105 CAKGGPALTLRTWH----VREWNGFVFVWQNADGLAPtwELPDVDM 146
Cdd:cd03479   101 SEPPDSQLKQKVRQpaypVRERGGLVWAYMGPAEEAP--EFPRYDW 144

Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1966960394  26 WFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAH-LGHG--GTVDGEQIV-CPFH--HYAYgPDGr 99
Cdd:cd03529     1 WQTVCALDDLPPGSGVAALVGDTQIAIFRLPGREVYAVQNMDPHSRANvLSRGivGDIGGEPVVaSPLYkqHFSL-KTG- 78

                          90       100
                  ....*....|....*....|....*....
gi 1966960394 100 riaaRCaKGGPALTLRTWHVREWNGFVFV 128
Cdd:cd03529    79 ----RC-LEDEDVSVATFPVRVEDGEVYV 102

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 1966960394  26 WFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVAcAVDAYCPHQGAHLGHGGtVDGEQIVCPFH----HYaygPDGRri 101
Cdd:cd03528     1 WVRVCAVDELPEGEPKRVDVGGRPIAVYRVDGEFY-ATDDLCTHGDASLSEGY-VEGGVIECPLHggrfDL---RTGK-- 73

                          90       100
                  ....*....|....*....|....*....
gi 1966960394 102 aarcAKGGPALT-LRTWHVREWNGFVFVW 129
Cdd:cd03528    74 ----ALSLPATEpLKTYPVKVEDGDVYVD 98

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).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1966960394  20 LPYPDG----WFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHGGTVDGeQIVCPFHHYAYG 95
Cdd:cd04337     8 LELEPGlrnfWYPVEFSKDLKMDTMVPFELFGQPWVLFRDEDGTPGCIRDECAHRACPLSLGKVIEG-RIQCPYHGWEYD 86

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1966960394  96 PDG---RRIAARCAKGGpaltLRTWHVREWNGFVFVWQNADGLAPT 138
Cdd:cd04337    87 GDGectKMPSTKCLNVG----IAALPCMEQDGMIWVWPGDDPPAAL 128

Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1966960394  47 GRDVVLYRTASGVACAVDAYCPHQGAHLgHGGTVDGEQIVCPFH 90
Cdd:cd03530    22 GGEIAVFRTADDEVFALENRCPHKGGPL-SEGIVHGEYVTCPLH 64

chlorophyllide a oxygenase

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1966960394   6 RAMHAVGPIDETAPlPYPDGWFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVACAVDAYCPHQGAHLGHGgTVDGEQI 85
Cdd:PLN02281  202 KSLNVSGPVPPYSP-HLKNFWYPVAFTADLKHDTMVPIECFEQPWVIFRGEDGKPGCVRNTCAHRACPLDLG-TVNEGRI 279

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1966960394  86 VCPFHHYAYGPDGRriaarcAKGGPALTLRTWHVR-----EWNGFVFVWQNADGLAPT 138
Cdd:PLN02281  280 QCPYHGWEYSTDGE------CKKMPSTKLLKVKIKslpclEQEGMIWIWPGDEPPAPI 331

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 1966960394  21 PYPDG-------WFALCFSRELKRGAVLTAPFMGRDVVLYRTASGVACAVDAyCPHQGAHLGHGGTVDGEQ-IVCPFHHY 92
Cdd:cd03548     3 PYIDAkwgfrnhWYPALFSHELEEGEPKGIQLCGEPILLRRVDGKVYALKDR-CLHRGVPLSKKPECFTKGtITCWYHGW 81

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1966960394  93 AYGPDGRRIAARCAKGGPAL----TLRTWHVREWNGFVFVW 129
Cdd:cd03548    82 TYRLDDGKLVTILANPDDPLigrtGLKTYPVEEAKGMIFVF 122