Aromatic-ring-hydroxylating dioxygenases
Encyclopedia
Aromatic-ring-hydroxylating dioxygenases (ARHD) incorporate two atoms of dioxygen (O2) into their substrates in the dihydroxylation reaction. The product is (substituted) cis-1,2-dihydroxycyclohexadiene, which is subsequently converted to (substituted) benzene glycol by a cis-diol dehydrogenase.
A large family of multicomponent mononuclear (non-heme) iron oxygenases has been identified. Components of bacterial aromatic-ring dioxygenases constitute two different functional classes: hydroxylase components and electron transfer components. Hydroxylase components are either (αβ)n or (α)n oligomers. Two prosthetic groups, a Rieske-type
[Fe2S2] center and a mononuclear iron, are associated with the α-subunit in the (αβ)n-type enzymes. Electron transfer components are composed of flavoprotein (NADH:ferredoxin oxidoreductase) and Rieske-type [Fe2S2] ferredoxin. In benzoate and toluate 1,2-dioxygenase systems, a single protein containing reductase and Rieske-type ferredoxin domains transfers the electrons from NADH to the hydroxylase component. In the phthalate 4,5-dioxygenase system, phthalate dioxygenase reductase (PDR) has the same function. PDR is a single protein comprising FMN
-binding reductase and plant-type ferredoxin domains. Thus, the electron transfer in ARHD systems can be summarised as:
phthalate 4,5-dioxygenase
4-sulfobenzoate 3,4-dioxygenase
4-chlorophenylacetate 3,4-dioxygenase
benzoate 1,2-dioxygenase
toluene dioxygenase
naphthalene 1,2-dioxygenase
terephthalate 1,2-dioxygenase
biphenyl 2,3-dioxygenase
has been determined. The protein is an (αβ)3 hexamer. The β-subunit belongs to the
α+β class. It has no prosthetic groups and its role in catalysis is unknown. The α-subunit can be divided into two domains: a Rieske domain that contains the [Fe2S2] center and the catalytic domain that contains the active site mononuclear iron. The Rieske domain (residues 38-158) consists of four β-sheets. The overall fold is very similar to that of the soluble fragment of the Rieske protein from bovine heart mitochondrial cytochrome bc1 complex. In the [Fe2S2] center, Fe1 is coordinated by two cysteine
residues (Cys-81 and Cys-101) while Fe2 is coordinated by Nδ atoms of two histidine
residues (His-83 and His-104). The catalytic domain belongs to the α+β class and is dominated by a nine-stranded antiparallel β-sheet. The iron of the active site is located at the bottom of a narrow channel, approximately 15 Å from the protein surface. The mononuclear iron is coordinated by His-208, His-213, Asp-362 (bidentate) and a water molecule. The geometry can be described as a distorted octahedral with one ligand missing. The structure of the hexamer suggests cooperativity between adjacent α-subunits, where electrons from the [Fe2S2] center in one α-subunit (A) are transferred to the mononuclear iron in the adjacent α-subunit (B) through AspB-205, which is hydrogen-bonded to HisA-104 of the Rieske center and HisB-208 of the active site.
A large family of multicomponent mononuclear (non-heme) iron oxygenases has been identified. Components of bacterial aromatic-ring dioxygenases constitute two different functional classes: hydroxylase components and electron transfer components. Hydroxylase components are either (αβ)n or (α)n oligomers. Two prosthetic groups, a Rieske-type
Rieske protein
Rieske proteins are iron-sulfur protein components of cytochrome bc1 complexes and cytochrome b6f complexes which were first discovered and isolated by John S. Rieske and co-workers in 1964. It is a unique [2Fe-2S] cluster in that one of the two Fe atoms is coordinated by two histidine residues...
[Fe2S2] center and a mononuclear iron, are associated with the α-subunit in the (αβ)n-type enzymes. Electron transfer components are composed of flavoprotein (NADH:ferredoxin oxidoreductase) and Rieske-type [Fe2S2] ferredoxin. In benzoate and toluate 1,2-dioxygenase systems, a single protein containing reductase and Rieske-type ferredoxin domains transfers the electrons from NADH to the hydroxylase component. In the phthalate 4,5-dioxygenase system, phthalate dioxygenase reductase (PDR) has the same function. PDR is a single protein comprising FMN
FMN
FMN may refer to several things:* Flavin mononucleotide.* Forsvarsministeriet, the Danish Ministry of Defence.* Four Corners Regional Airport outside Farmington, New Mexico, its IATA airport code.* Fluid Music....
-binding reductase and plant-type ferredoxin domains. Thus, the electron transfer in ARHD systems can be summarised as:
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FAD or FMN |
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[Fe2S2] |
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[Fe2S2], Fe |
Biochemical classification
benzene 1,2-dioxygenase- benzene + NADH + H+ + O2 = cis-cyclohexa-3,5-diene-1,2-diol + NAD+
phthalate 4,5-dioxygenase
- phthalate + NADH + H+ + O2 = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate + NAD+
4-sulfobenzoate 3,4-dioxygenase
- 4-sulfobenzoate + NADH + H+ + O2 = 3,4-dihydroxybenzoate + sulfite + NAD+
4-chlorophenylacetate 3,4-dioxygenase
- 4-chlorophenylacetate + NADH + H+ + O2 = 3,4-dihydroxyphenylacetate + chloride + NAD+
benzoate 1,2-dioxygenase
- benzoate + NADH + H+ + O2 = 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate + NAD+
toluene dioxygenase
- toluene + NADH + H+ + O2 = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD+
naphthalene 1,2-dioxygenase
- naphthalene + NADH + H+ + O2 = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD+
terephthalate 1,2-dioxygenase
- terephthalate + NADH + H+ + O2 = (1R,6S)-dihydroxycyclohexa-2,4-diene-1,4-dicarboxylate + NAD+
biphenyl 2,3-dioxygenase
- biphenyl + NADH + H+ + O2 = (1S,2R)-3-phenylcyclohexa-3,5-diene-1,2-diol + NAD+
Structure
The crystal structure of the hydroxylase component of naphthalene 1,2-dioxygenase from PseudomonasPseudomonas
Pseudomonas is a genus of gammaproteobacteria, belonging to the family Pseudomonadaceae containing 191 validly described species.Recently, 16S rRNA sequence analysis has redefined the taxonomy of many bacterial species. As a result, the genus Pseudomonas includes strains formerly classified in the...
has been determined. The protein is an (αβ)3 hexamer. The β-subunit belongs to the
α+β class. It has no prosthetic groups and its role in catalysis is unknown. The α-subunit can be divided into two domains: a Rieske domain that contains the [Fe2S2] center and the catalytic domain that contains the active site mononuclear iron. The Rieske domain (residues 38-158) consists of four β-sheets. The overall fold is very similar to that of the soluble fragment of the Rieske protein from bovine heart mitochondrial cytochrome bc1 complex. In the [Fe2S2] center, Fe1 is coordinated by two cysteine
Cysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...
residues (Cys-81 and Cys-101) while Fe2 is coordinated by Nδ atoms of two histidine
Histidine
Histidine Histidine, an essential amino acid, has a positively charged imidazole functional group. It is one of the 22 proteinogenic amino acids. Its codons are CAU and CAC. Histidine was first isolated by German physician Albrecht Kossel in 1896. Histidine is an essential amino acid in humans...
residues (His-83 and His-104). The catalytic domain belongs to the α+β class and is dominated by a nine-stranded antiparallel β-sheet. The iron of the active site is located at the bottom of a narrow channel, approximately 15 Å from the protein surface. The mononuclear iron is coordinated by His-208, His-213, Asp-362 (bidentate) and a water molecule. The geometry can be described as a distorted octahedral with one ligand missing. The structure of the hexamer suggests cooperativity between adjacent α-subunits, where electrons from the [Fe2S2] center in one α-subunit (A) are transferred to the mononuclear iron in the adjacent α-subunit (B) through AspB-205, which is hydrogen-bonded to HisA-104 of the Rieske center and HisB-208 of the active site.