Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1

Akira Nakamura, Masahiro Fujihashi, Riku Aono, Takaaki Sato, Yosuke Nishiba, Shosuke Yoshida, Ayumu Yano, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki*

*この研究の対応する著者

研究成果: Article査読

19 被引用数 (Scopus)

抄録

Ribose-1,5-bisphosphate isomerase (R15Pi) is a novel enzyme recently identified as a member of an AMP metabolic pathway in archaea. The enzyme converts D-ribose 1,5-bisphosphate into ribulose 1,5-bisphosphate, providing the substrate for archaeal ribulose-1,5-bisphosphate carboxylase/oxygenases. We here report the crystal structures of R15Pi from Thermococcus kodakarensis KOD1 (Tk-R15Pi) with and without its substrate or product. Tk-R15Pi is a hexameric enzyme formed by the trimerization of dimer units. Biochemical analyses show that Tk-R15Pi only accepts the α-anomer of D-ribose 1,5-bisphosphate and that Cys 133 and Asp 202 residues are essential for ribulose 1,5-bisphosphate production. Comparison of the determined structures reveals that the unliganded and product-binding structures are in an open form, whereas the substrate-binding structure adopts a closed form, indicating domain movement upon substrate binding. The conformational change to the closed form optimizes active site configuration and also isolates the active site from the solvent, which may allow deprotonation of Cys 133and protonation of Asp 202 to occur. The structural features of the substrate-binding form and biochemical evidence lead us to propose that the isomerase reaction proceeds via a cis-phosphoenolate intermediate.

本文言語English
ページ(範囲)20784-20796
ページ数13
ジャーナルJournal of Biological Chemistry
287
25
DOI
出版ステータスPublished - 2012 6月 15
外部発表はい

ASJC Scopus subject areas

  • 生化学
  • 分子生物学
  • 細胞生物学

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