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J. Biol. Chem., Vol. 280, Issue 22, 21144-21154, June 3, 2005

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Crystal Structure of the Hydroxyquinol 1,2-Dioxygenase from Nocardioides simplex 3E, a Key Enzyme Involved in Polychlorinated Aromatics Biodegradation^*

Marta Ferraroni, Jana Seifert, Vasili M. Travkin¶, Monika Thiel, Stefan Kaschabek, Andrea Scozzafava, Ludmila Golovleva¶, Michael Schlömann, and Fabrizio Briganti||

From the Dipartimento di Chimica, Università di Firenze, Via della Lastruccia 3, Sesto Fiorentino I-50019, Italy, the TU Bergakademie Freiberg Interdisziplinäres Ökologisches Zentrum, Freiberg D-09599, Germany, and the ^¶Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino Moscow Region 142290, Russia

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 Å 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.

Received for publication, January 19, 2005 , and in revised form, March 10, 2005.

^* This work was supported by Grant ICA2-CT-2000-10006 from the European Commission Research and Technological Development Program Copernicus, Contract HPRI-CT-1999-00017 from the European Community Access to Research Infrastructure Action of the Improving Human Potential Program to the EMBL Hamburg outstation, and Grant COFIN2002 from the Italian Ministero Università e Ricerca Scientifica. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The atomic coordinates and structure factors (code 1TMX) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^|| To whom correspondence should be addressed. Fax: 39-055-457-3333; E-mail: fabrizio.briganti{at}unifi.it.

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