START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 3170521   73 GAELVGPPMKSILKCNWKVPTENFVGDGYHVGWTHASALHVLGGELGglagnqAEMPFDELGIQVTTR-HGHGFGVIDna 151
Cdd:cd08881   1 GLEVVGGPQKWVIKANWKLAAENFAGDGYHTGTTHASALEAGLPPDA------ADLPPIDLGLQFTAPwHGHGLGFFL-- 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 3170521  152 aiaihakrdeyakymeetipkvaenlgepraklfNGHWNCSTFPNCSFLYG-TNIFKV 208
Cdd:cd08881  73 ----------------------------------DSPQHGTIFPNLSFLPGyFNTLRV 96

C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). This domain binds non-heme Fe(II). 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 form 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. Proteins belonging to this subgroup include the terminal oxygenase alpha subunits of biphenyl dioxygenase, cumene dioxygenase from Pseudomonas fluorescens IP01, ethylbenzene dioxygenase, naphthalene 1,2-dioxygenase, nitrobenzene dioxygenase from Comamonas sp. strain JS765, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, and the polycyclic aromatic hydrocarbons (PAHs)degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. 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 3170521   73 GAELVGPPMKSILKCNWKVPTENFVGDGYHVGWTHASALHVLGGELGglagnqAEMPFDELGIQVTTR-HGHGFGVIDna 151
Cdd:cd08881   1 GLEVVGGPQKWVIKANWKLAAENFAGDGYHTGTTHASALEAGLPPDA------ADLPPIDLGLQFTAPwHGHGLGFFL-- 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 3170521  152 aiaihakrdeyakymeetipkvaenlgepraklfNGHWNCSTFPNCSFLYG-TNIFKV 208
Cdd:cd08881  73 ----------------------------------DSPQHGTIFPNLSFLPGyFNTLRV 96

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
                ....*....|....*....|....*....|....*....|....*....|.
gi 3170521    2 FSTDGKLVDVPLREKCYhdELDRDSLSLKTIRVESYRGFVFGCFDETAPSL 52
Cdd:cd03469  70 YDLDGKLVGVPREEGFP--GFDKEKLGLRTVPVEEWGGLIFVNLDPDAPPL 118

C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related aromatic ring hydroxylating dioxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of naphthalene 1,2-dioxygenase (NDO) and related Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs, also known as aromatic ring hydroxylating dioxygenases). This domain binds non-heme Fe(II). 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 form 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. Proteins belonging to this subgroup include the terminal oxygenase alpha subunits of biphenyl dioxygenase, cumene dioxygenase from Pseudomonas fluorescens IP01, ethylbenzene dioxygenase, naphthalene 1,2-dioxygenase, nitrobenzene dioxygenase from Comamonas sp. strain JS765, toluene 2,3-dioxygenase from Pseudomonas putida F1, dioxin dioxygenase of Sphingomonas sp. Strain RW1, and the polycyclic aromatic hydrocarbons (PAHs)degrading ring-hydroxylating dioxygenase from Sphingomonas CHY-1. 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 3170521   73 GAELVGPPMKSILKCNWKVPTENFVGDGYHVGWTHASALHVLGGELGglagnqAEMPFDELGIQVTTR-HGHGFGVIDna 151
Cdd:cd08881   1 GLEVVGGPQKWVIKANWKLAAENFAGDGYHTGTTHASALEAGLPPDA------ADLPPIDLGLQFTAPwHGHGLGFFL-- 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 3170521  152 aiaihakrdeyakymeetipkvaenlgepraklfNGHWNCSTFPNCSFLYG-TNIFKV 208
Cdd:cd08881  73 ----------------------------------DSPQHGTIFPNLSFLPGyFNTLRV 96

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
                ....*....|....*....|....*....|....*....|....*....|.
gi 3170521    2 FSTDGKLVDVPLREKCYhdELDRDSLSLKTIRVESYRGFVFGCFDETAPSL 52
Cdd:cd03469  70 YDLDGKLVGVPREEGFP--GFDKEKLGLRTVPVEEWGGLIFVNLDPDAPPL 118

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
                ....*....|....*....|....*....|....*....|....*....|...
gi 3170521    1 VFSTDGKLVDVPLREKCYHDELDRDSLSLKTI-RVESYRGFVFGCFDETAPSL 52
Cdd:cd03535  71 TYRNTGRLVGVPAQQEAYGGGFDKSQWGLRPApNLDSYNGLIFGSLDPKAPSL 123

Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). 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. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is intermediate in size between ethylbenzene and biphenyl. NBDO catalyzes the initial reaction in nitrobenzene degradation, oxidizing the aromatic rings of mono- and dinitrotoluenes to form catechol and nitrite. NBDO belongs to the naphthalene subfamily of ROs. AkbDO is involved in alkylbenzene catabolism, converting o-xylene to 2,3- and 3,4-dimethylphenol and ethylbenzene to cis-dihydrodiol. DFDO is involved in dibenzofuran degradation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 3170521    2 FSTDGKLVDVPLREKCYHDELDRDSLSLKTIRVESYRGFVFGCFDETAPSL 52
Cdd:cd03472  78 YDTAGNLVNVPFEKEAFCDGLDKADWGPLQARVETYKGLIFANWDAEAPDL 128

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
                ....*....|....*....|....*...
gi 3170521   86 KCNWKVPTENFVgDGYHVGWTHASALHV 113
Cdd:cd00680   8 DCNWKLAVENFL-ECYHVPTVHPDTLAT 34

C-terminal catalytic domain of Pseudomonas fluorescens MupW and related aromatic ring hydroxylating dioxygenases; C-terminal catalytic domain of the oxygenase alpha subunit of Pseudomonas fluorescens MupW 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 a C-terminal domain which binds the non-heme Fe(II). The Fe(II) is co-ordinated by conserved His and Asp residues. MupW is part of the mupirocin biosynthetic gene cluster in Pseudomonas fluorescens, and may catalyze the oxidation of the 16-methyl group during biosynthesis of this polyketide antibiotic. Mupirocin is a mixture of pseudomonic acids which targets isoleucyl-tRNA synthase and is a strong inhibitor of Gram positive bacterial and mycoplasmal pathogens. 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
                ....*....|....*....|....
gi 3170521   84 ILKCNWKVPTENFVgDGYHVGWTH 107
Cdd:cd08882   7 VLPCNWKVAQEAFN-ESYHVPTTH 29