3VM6

Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1 in complex with alpha-D-ribose-1,5-bisphosphate

Summary for 3VM6

• Entry DOI: 10.2210/pdb3vm6/pdb
• Related: 3A11 3A9C
• Descriptor: Translation initiation factor eIF-2B, delta subunit, 1,5-di-O-phosphono-alpha-D-ribofuranose, DI(HYDROXYETHYL)ETHER, ... (7 entities in total)
• Functional Keywords: rossmann fold, hexamer, isomerase, amp metabolism, sugar binding
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 3
• Total formula weight: 117451.44

Authors

Nakamura, A.,Fujihashi, M.,Aono, R.,Sato, T.,Nishiba, Y.,Yoshida, S.,Yano, A.,Atomi, H.,Imanaka, T.,Miki, K. (deposition date: 2011-12-08, release date: 2012-04-25, Last modification date: 2023-11-08)

Primary citation

Nakamura, A.,Fujihashi, M.,Aono, R.,Sato, T.,Nishiba, Y.,Yoshida, S.,Yano, A.,Atomi, H.,Imanaka, T.,Miki, K.
Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1
J.Biol.Chem., 287:20784-20796, 2012

PubMed 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(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.

PubMed: 22511789
DOI: 10.1074/jbc.M112.349423

Experimental method

X-RAY DIFFRACTION (2.85 Å)