Aromatic-ring-hydroxylating dioxygenases

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.

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• 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