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J. Biol. Chem., Vol. 278, Issue 22, 20313-20318, May 30, 2003

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Crystal Structure of Rice -Galactosidase Complexed with D-Galactose^*

Zui Fujimoto , Satoshi Kaneko , Mitsuru Momma , Hideyuki Kobayashi  and Hiroshi Mizuno  ¶

From the Department of Biochemistry, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan and the Biological Function Division, National Food Research Institute, Tsukuba, Ibaraki 305-8642, Japan

-Galactosidases catalyze the hydrolysis of -1,6-linked galactosyl residues from galacto-oligosaccharides and polymeric galacto-(gluco)mannans. The crystal structure of rice -galactosidase has been determined at 1.5Å resolution using the multiple isomorphous replacement method. The structure consisted of a catalytic domain and a C-terminal domain and was essentially the same as that of -N-acetylgalactosaminidase, which is the same member of glycosyl hydrolase family 27. The catalytic domain had a (/)₈-barrel structure, and the C-terminal domain was made up of eight -strands containing a Greek key motif. The structure was solved as a complex with D-galactose, providing a mode of substrate binding in detail. The D-galactose molecule was found bound in the active site pocket on the C-terminal side of the central -barrel of the catalytic domain. The D-galactose molecule consisted of a mixture of two anomers present in a ratio equal to their natural abundance. Structural comparisons of rice -galactosidase with chicken -N-acetylgalactosaminidase provided further understanding of the substrate recognition mechanism in these enzymes.

Received for publication, March 5, 2003 , and in revised form, March 20, 2003.

^* This work was performed with the approval of the Photon Factory, the High Energy Accelerator Research Organization, Japan (proposal number 2000G294) and SPring-8 (proposal number 2002A0130-NL1-np) and supported in part by Rice Genome Project Grants PR-2106 and PR-2206, Ministry of Agriculture, Forestry, and Fisheries, Japan. 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.

^¶ To whom correspondence should be addressed: Dept. of Biochemistry, National Inst. of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan, Tel.: 81-29-838-7014; Fax: 81-29-838-7408; E-mail: mizuno{at}affrc.go.jp.

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