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

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

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.

Original languageEnglish
Pages (from-to)20784-20796
Number of pages13
JournalJournal of Biological Chemistry
Volume287
Issue number25
DOIs
Publication statusPublished - 2012 Jun 15
Externally publishedYes

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Isomerases
Ligands
Substrates
Ribose
Catalytic Domain
Enzymes
Oxygenases
Deprotonation
Protonation
Archaea
Adenosine Monophosphate
Metabolic Networks and Pathways
Dimers
Crystal structure
Thermococcus kodakarensis ribose-1,5-bisphosphate isomerase
ribose-1,5-bisphosphate
ribulose-1,5 diphosphate

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1. / Nakamura, Akira; Fujihashi, Masahiro; Aono, Riku; Sato, Takaaki; Nishiba, Yosuke; Yoshida, Shosuke; Yano, Ayumu; Atomi, Haruyuki; Imanaka, Tadayuki; Miki, Kunio.

In: Journal of Biological Chemistry, Vol. 287, No. 25, 15.06.2012, p. 20784-20796.

Research output: Contribution to journalArticle

Nakamura, A, Fujihashi, M, Aono, R, Sato, T, Nishiba, Y, Yoshida, S, Yano, A, Atomi, H, Imanaka, T & Miki, K 2012, 'Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1', Journal of Biological Chemistry, vol. 287, no. 25, pp. 20784-20796. https://doi.org/10.1074/jbc.M112.349423
Nakamura, Akira ; Fujihashi, Masahiro ; Aono, Riku ; Sato, Takaaki ; Nishiba, Yosuke ; Yoshida, Shosuke ; Yano, Ayumu ; Atomi, Haruyuki ; Imanaka, Tadayuki ; Miki, Kunio. / Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1. In: Journal of Biological Chemistry. 2012 ; Vol. 287, No. 25. pp. 20784-20796.
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