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Published online before print December 29, 2005
Protein Science, DOI: 10.1110/ps.051922406
 Copyright © 2005 The Protein Society
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PROTEIN STRUCTURE REPORT

Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3

Ryoichi Arai1,2, Mutsuko Kukimoto-Niino1, Chizu Kuroishi2, Yoshitaka Bessho1, Mikako Shirouzu1,2 and Shigeyuki Yokoyama1,2,3

1 Protein Research Group, RIKEN Genomic Sciences Center, Tsurumi, Yokohama 230-0045, Japan
2 RIKEN Harima Institute at SPring-8, Sayo, Hyogo 679-5148, Japan
3 Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan

(RECEIVED October 20, 2005; FINAL REVISION October 20, 2005; ACCEPTED November 2, 2005)

PH0459, from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, is a probable haloacid dehalogenase with a molecular mass of 26,725 Da. Here, we report the 2.0 Å crystal structure of PH0459 (PDB ID: 1X42) determined by the multiwavelength anomalous dispersion method. The core domain has an {alpha}/{beta} structure formed by a six-stranded parallel {beta}-sheet flanked by six {alpha}-helices and three 310-helices. One disulfide bond, Cys186–Cys212, forms a bridge between an {alpha}-helix and a 310-helix, although PH0459 seems to be an intracellular protein. The subdomain inserted into the core domain has a four-helix bundle structure. The crystal packing suggests that PH0459 exists as a monomer. A structural homology search revealed that PH0459 resembles the L-2-haloacid dehalogenases L-DEX YL from Pseudomonas sp. YL and DhlB from Xanthobacter autotrophicus GJ10. A comparison of the active sites suggested that PH0459 probably has haloacid dehalogenase activity, but its substrate specificity may be different. In addition, the disulfide bond in PH0459 probably facilitates the structural stabilization of the neighboring region in the monomeric form, although the corresponding regions in L-DEX YL and DhlB may be stabilized by dimerization. Since heat-stable dehalogenases can be used for the detoxification of halogenated aliphatic compounds, PH0459 will be a useful target for biotechnological research.

Keywords: haloacid dehalogenase; HAD superfamily; hydrolase; detoxification; intracellular disulfide bond; hyperthermophilic archaeon; structural genomics

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051922406.

Reprint requests to: Shigeyuki Yokoyama, Protein Research Group, Genomic Sciences Center, RIKEN Yokohama Institute, 1-7-22, Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan; e-mail: yokoyama{at}biochem.s.u-tokyo.ac.jp; fax: 81-45-503-9195.


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