1. Biochemical classification

2. Structure

3. References

4. External links

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:

Biochemical classification

benzene + NADH + H⁺ + O₂ = cis-cyclohexa-3,5-diene-1,2-diol + NAD⁺

phthalate + NADH + H⁺ + O₂ = cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate + NAD⁺

4-sulfobenzoate + NADH + H⁺ + O₂ = 3,4-dihydroxybenzoate + sulfite + NAD⁺

4-chlorophenylacetate + NADH + H⁺ + O₂ = 3,4-dihydroxyphenylacetate + chloride + NAD⁺

benzoate + NADH + H⁺ + O₂ = 1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate + NAD⁺

toluene + NADH + H⁺ + O₂ = (1S,2R)-3-methylcyclohexa-3,5-diene-1,2-diol + NAD⁺

naphthalene + NADH + H⁺ + O₂ = (1R,2S)-1,2-dihydronaphthalene-1,2-diol + NAD⁺

terephthalate + NADH + H⁺ + O₂ = (1R,6S)-dihydroxycyclohexa-2,4-diene-1,4-dicarboxylate + NAD⁺

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 Pseudomonas 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 N^δ 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 Asp_B-205, which is hydrogen-bonded to His_A-104 of the Rieske center and His_B-208 of the active site.

References

• {{cite journal | author=Harayama, S. |author2=Kok, M. |author3=Neidle, E.L. |last-author-amp=yes | title=Functional and evolutionary relationships among diverse oxygenases | journal=Annu. Rev. Microbiol. | year=1992 | volume=46 | pages=565–601 | pmid=1444267 | doi=10.1146/annurev.mi.46.100192.003025}}
• {{cite journal |author1=Butler, C.S. |author2=Mason, J.R. |lastauthoramp=yes | title=Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases | journal=Adv. Microb. Physiol. | year=1997 | volume=38 | pages=47–84 | pmid=8922118 | doi=10.1016/S0065-2911(08)60155-1 | series=Advances in Microbial Physiology | isbn=978-0-12-027738-4}}
• {{cite journal | author=Jiang, H. |author2=Parales, R.E. |author3=Lynch, N.A. |author4=Gibson, D.T. |last-author-amp=yes | title=Site-directed mutagenesis of conserved amino acids in the alpha subunit of toluene dioxygenase: potential mononuclear non-heme iron coordination sites | journal=J. Bacteriol. | year=1996 | volume=178 | pages=3133–3139 | pmid=8655491 | issue=11 | pmc=178063}}
• {{cite journal | author=Kauppi, B. |author2=Lee, K. |author3=Carredano, E. |author4=Parales, R.E. |author5=Gibson, D.T. |author6=Eklund, H. |author7=Ramaswamy, S. |last-author-amp=yes | title=Structure of an aromatic-ring-hydroxylating dioxygenase – naphthalene 1,2-dioxygenase | journal=Structure | year=1998 | volume=6 | pages=571–586 | pmid=9634695 | doi=10.1016/S0969-2126(98)00059-8 | issue=5}}

External links

• {{PDB|1NDO}} - structure of naphthalene 1,2-dioxygenase from Pseudomonas putida
• {{PDB|1ULI}} - structure of biphenyl 2,3-dioxygenase from Rhodococcus sp. strain RHA1
• {{InterPro|IPR001663}} - InterPro entry for Bacterial ring hydroxylating dioxygenase, alpha subunit

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