1TMX

Crystal structure of hydroxyquinol 1,2-dioxygenase from Nocardioides Simplex 3E

Summary for 1TMX

• Entry DOI: 10.2210/pdb1tmx/pdb
• Descriptor: hydroxyquinol 1,2-dioxygenase, FE (III) ION, COPPER (II) ION, ... (8 entities in total)
• Functional Keywords: beta barrel, oxidoreductase
• Biological source: Pimelobacter simplex
• Total number of polymer chains: 2
• Total formula weight: 66064.12

Authors

Ferraroni, M.,Travkin, V.M.,Seifert, J.,Schlomann, M.,Golovleva, L.,Scozzafava, A.,Briganti, F. (deposition date: 2004-06-11, release date: 2005-03-22, Last modification date: 2024-02-14)

Primary citation

Ferraroni, M.,Seifert, J.,Travkin, V.M.,Thiel, M.,Kaschabek, S.,Scozzafava, A.,Golovleva, L.,Schlomann, M.,Briganti, F.
Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation.
J.Biol.Chem., 280:21144-21154, 2005

PubMed Abstract: Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a central intermediate in the degradation of aromatic compounds including a variety of particularly recalcitrant polychloro- and nitroaromatic pollutants. We report here the primary sequence determination and the analysis of the crystal structure of the 1,2-HQD from Nocardioides simplex 3E solved at 1.75 A resolution using the multiple wavelength anomalous dispersion of the two catalytic irons (1 Fe/293 amino acids). The catalytic Fe(III) coordination polyhedron composed by the side chains of Tyr164, Tyr197, His221, and His223 resembles that of the other known intradiol-cleaving dioxygenases, but several of the tertiary structure features are notably different. One of the most distinctive characteristics of the present structure is the extensive openings and consequent exposure to solvent of the upper part of the catalytic cavity arranged to favor the binding of hydroxyquinols but not catechols. A co-crystallized benzoate-like molecule is also found bound to the metal center forming a distinctive hydrogen bond network as observed previously also in 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP. This is the first structure of an intradiol dioxygenase specialized in hydroxyquinol ring cleavage to be investigated in detail.

PubMed: 15772073
DOI: 10.1074/jbc.M500666200

Experimental method

X-RAY DIFFRACTION (1.75 Å)