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J. Biol. Chem., Vol. 281, Issue 45, 34365-34373, November 10, 2006

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Crystal Structures of Nonoxidative Zinc-dependent 2,6-Dihydroxybenzoate (-Resorcylate) Decarboxylase from Rhizobium sp. Strain MTP-10005^*

Masaru Goto, Hideyuki Hayashi, Ikuko Miyahara, Ken Hirotsu¹, Masahiro Yoshida^¶, and Tadao Oikawa^¶||

From the Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan, Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558-8585, Japan, ^¶Department of Biotechnology, Faculty of Engineering, Kansai University, and the ^||Kansai University High Technology Research Center, Osaka 564-8680, Japan

Reversible 2,6-dihydroxybenzoate decarboxylase from Rhizobium sp. strain MTP-10005 belongs to a nonoxidative decarboxylase family. We have determined the structures of the following three forms of the enzyme: the native form, the complex with the true substrate (2,6-dihydroxybenzoate), and the complex with 2,3-dihydroxybenzaldehyde at 1.7-, 1.9-, and 1.7-Å resolution, respectively. The enzyme exists as a tetramer, and the subunit consists of one ()₈ triose-phosphate isomerase-barrel domain with three functional linkers and one C-terminal tail. The native enzyme possesses one Zn²⁺ ion liganded by Glu⁸, His¹⁰, His¹⁶⁴, Asp²⁸⁷, and a water molecule at the active site center, although the enzyme has been reported to require no cofactor for its catalysis. The substrate carboxylate takes the place of the water molecule and is coordinated to the Zn²⁺ ion. The 2-hydroxy group of the substrate is hydrogen-bonded to Asp²⁸⁷, which forms a triad together with His²¹⁸ and Glu²²¹ and is assumed to be the catalytic base. On the basis of the geometrical consideration, substrate specificity is uncovered, and the catalytic mechanism is proposed for the novel Zn²⁺-dependent decarboxylation.

Received for publication, August 1, 2006 , and in revised form, September 1, 2006.

The atomic coordinates and structure factors (code 2DVT, 2DVU, and 2DVX) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by the National Project on Protein Structural and Functional Analyses and in part by research grants from the Japan Foundation of Applied Enzymology and the Kansai University High Technology Research Center. 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.

¹ To whom correspondence should be addressed. Tel.: 81-6-6605-3129; Fax: 81-6-6605-2557; E-mail: hirotsu{at}sci.osaka-cu.ac.jp.

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This article has been cited by other articles:

				M. Yoshida, T. Oikawa, H. Obata, K. Abe, H. Mihara, and N. Esaki Biochemical and Genetic Analysis of the {gamma}-Resorcylate (2,6-Dihydroxybenzoate) Catabolic Pathway in Rhizobium sp. Strain MTP-10005: Identification and Functional Analysis of Its Gene Cluster J. Bacteriol., March 1, 2007; 189(5): 1573 - 1581. [Abstract] [Full Text] [PDF]