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 495852251   6 PTTLATLMQIPDAGFLEVEallESGAESLVLYREGTQVRAWLNICPHAGRRLDWAPGQflktkEGQLVCAAHGAAFELSG 85
Cdd:cd03467    1 WVVVGALSELPPGGGRVVV---VGGGPVVVVRREGGEVYALSNRCTHQGCPLSEGEGE-----DGCIVCPCHGSRFDLRT 72

                         90       100
                 ....*....|....*....|....*..
gi 495852251  86 GECVSGPCRGQsLFAVPVRVEDEQVLL 112
Cdd:cd03467   73 GEVVSGPAPRP-LPKYPVKVEGDGVVW 98

nitrite reductase [NAD(P)H], small subunit; This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused. [Central intermediary metabolism, Nitrogen metabolism]

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495852251   30 GAESLVLYR-EGTQVRAWLNICPHaGRRLDWAPGqFLKTKEGQLV--CAAHGAAFELSGGECVSGPcrGQSLFAVPVRVE 106
Cdd:TIGR02378  22 GDTQIAIFRvPGDQVFAIQNMCPH-KRAFVLSRG-IVGDAQGELWvaCPLHKRNFRLEDGRCLEDD--SGSVRTYEVRVE 97

                  ....*..
gi 495852251  107 DEQVLLG 113
Cdd:TIGR02378  98 DGRVYVA 104

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 495852251   6 PTTLATLMQIPDAGFLEVEallESGAESLVLYREGTQVRAWLNICPHAGRRLDWAPGQflktkEGQLVCAAHGAAFELSG 85
Cdd:cd03467    1 WVVVGALSELPPGGGRVVV---VGGGPVVVVRREGGEVYALSNRCTHQGCPLSEGEGE-----DGCIVCPCHGSRFDLRT 72

                         90       100
                 ....*....|....*....|....*..
gi 495852251  86 GECVSGPCRGQsLFAVPVRVEDEQVLL 112
Cdd:cd03467   73 GEVVSGPAPRP-LPKYPVKVEGDGVVW 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 495852251   14 QIPDAGFLEVEAllesGAESLVLYR-EGTQVRAWLNICPHAGRRLDWAPGqflkTKEGQLVCAAHGAAFELSgGECVSGP 92
Cdd:pfam00355  10 ELPEGEPKVVEV----GGEPLVVFRdEDGELYALEDRCPHRGAPLSEGKV----NGGGRLECPYHGWRFDGT-GKVVKVP 80

                  ....
gi 495852251   93 CRGQ 96
Cdd:pfam00355  81 APRP 84

AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495852251  14 QIPDAGFLEVEAllesGAESLVLYREGTQVRAWLNICPHAGrrldwAPgqfLKT---KEGQLVCAAHGAAFELSGGECVS 90
Cdd:cd03478    8 DLGDGEMKEVDV----GDGKVLLVRQGGEVHAIGAKCPHYG-----AP---LAKgvlTDGRIRCPWHGACFNLRTGDIED 75

                         90       100
                 ....*....|....*....|.
gi 495852251  91 GPCRgQSLFAVPVRVEDEQVL 111
Cdd:cd03478   76 APAL-DSLPCYEVEVEDGRVY 95

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 495852251   7 TTLATLMQIPDAGFLEVEAllesGAESLVLYREGTQVRAWLNICPHAGRRLdwAPGQFlktkEGQLV-CAAHGAAFELSG 85
Cdd:cd03528    2 VRVCAVDELPEGEPKRVDV----GGRPIAVYRVDGEFYATDDLCTHGDASL--SEGYV----EGGVIeCPLHGGRFDLRT 71

                         90       100
                 ....*....|....*....|....*..
gi 495852251  86 GECVSGPCRgQSLFAVPVRVEDEQVLL 112
Cdd:cd03528   72 GKALSLPAT-EPLKTYPVKVEDGDVYV 97

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 495852251  32 ESLVLYREGT-QVRAWLNICPHAGrrldwAPGQFLKTKEGQLVCAAHGAAFElSGGECVSGPCRGQSLFAVPVRV 105
Cdd:cd03532   27 EPVVLYRTQDgRVAALEDRCPHRS-----APLSKGSVEGGGLVCGYHGLEFD-SDGRCVHMPGQERVPAKACVRS 95

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 495852251  14 QIPDAGFLEVEALlesGAESLVLYREGT-QVRAWLNICPHAGRRLDWAPGQFLKTKegqlVCAAHGAAFELSGG------ 86
Cdd:cd03536    9 EIPNKGDFMVRDM---GSDSVIVARDKDgEIHVSLNVCPHRGMRISTTDGGNTQIH----VCIYHGWAFRPNGDfigapv 81

                         90
                 ....*....|
gi 495852251  87 --ECVSGPCR 94
Cdd:cd03536   82 ekECMHGKMR 91