AONO RIKU
Department / Course College of Life Sciences Department of Biotechnology
Title / Position Assistant Professor
Language English
Publication Date 2012/06
Type Research paper (scientific journal)
Peer Review Yes
Title Dynamic, Ligand-dependent Conformational Change Triggers Reaction of Ribose-1,5-bisphosphate Isomerase from Thermococcus kodakarensis KOD1
Journal JOURNAL OF BIOLOGICAL CHEMISTRY
Publisher AMER SOC BIOCHEMISTRY MOLECULAR BIOLOGY INC
Volume, Issue, Page 287(25),20784-20796
Author and coauthor Akira Nakamura,Masahiro Fujihashi,Riku Aono,Takaaki Sato,Yosuke Nishiba,Shosuke Yoshida,Ayumu Yano,Haruyuki Atomi,Tadayuki Imanaka,Kunio Miki
Details 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 alpha-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(133) and 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.
DOI 10.1074/jbc.M112.349423
ISSN 00219258
PMID 22511789
PermalinkURL http://www.jbc.org/content/287/25/20784.long