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Protein Science (2008), 17:126-135. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: Implications for catalytic mechanism

Haruka Tamura1, Yohtaro Saito2, Hiroki Ashida2, Tsuyoshi Inoue1,3, Yasushi Kai1, Akiho Yokota2, and Hiroyoshi Matsumura1,3

1 Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan
2 Department of Molecular Biology, Graduate School of Biological Science, Nara Institute of Science and Technology (NAIST), Nara 630-0101, Japan
3 CREST (Sosho Project), JST, Osaka 565-0871, Japan

(RECEIVED August 11, 2007; FINAL REVISION October 11, 2007; ACCEPTED October 11, 2007)

The methionine salvage pathway (MSP) plays a crucial role in recycling a sulphahydryl derivative of the nucleoside. Recently, the genes and reactions in MSP from Bacillus subtilis have been identified, where 5-methylthioribose 1-phosphate isomerase (M1Pi) catalyzes a conversion of 5-methylthioribose 1-phosphate (MTR-1-P) to 5-methylthioribulose 1-phosphate (MTRu-1-P). Herein, we report the crystal structures of B. subtilis M1Pi (Bs-M1Pi) in complex with its product MTRu-1-P, and a sulfate at 2.4 and 2.7 Å resolution, respectively. The electron density clearly shows the presence of each compound in the active site. The structural comparison with other homologous proteins explains how the substrate uptake of Bs-M1Pi may be induced by an open/closed transition of the active site. The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi.

Keywords: aldose–ketose isomerase; 5-methylthioribose 1-phosphate isomerase; open/closed transition; crystal structure


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