5GMD

Crystal structure of Sulfolobus solfataricus diphosphomevalonate decarboxylase in complex with ATP-gamma-S

Summary for 5GMD

• Entry DOI: 10.2210/pdb5gmd/pdb
• Related: 5GME
• Descriptor: Diphosphomevalonate decarboxylase, (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID, PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER, ... (6 entities in total)
• Functional Keywords: sulfolobus solfataricus, diphosphomevalonate decarboxylase, atprs, lyase
• Biological source: Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
• Total number of polymer chains: 1
• Total formula weight: 38450.26

Authors

Unno, H.,Hemmi, H.,Hattori, A. (deposition date: 2016-07-13, release date: 2016-12-28, Last modification date: 2024-11-06)

Primary citation

Motoyama, K.,Unno, H.,Hattori, A.,Takaoka, T.,Ishikita, H.,Kawaide, H.,Yoshimura, T.,Hemmi, H.
A Single Amino Acid Mutation Converts (R)-5-Diphosphomevalonate Decarboxylase into a Kinase
J. Biol. Chem., 292:2457-2469, 2017

PubMed Abstract: The biosynthesis of isopentenyl diphosphate, a fundamental precursor for isoprenoids, via the mevalonate pathway is completed by diphosphomevalonate decarboxylase. This enzyme catalyzes the formation of isopentenyl diphosphate through the ATP-dependent phosphorylation of the 3-hydroxyl group of ()-5-diphosphomevalonate followed by decarboxylation coupled with the elimination of the 3-phosphate group. In this reaction, a conserved aspartate residue has been proposed to be involved in the phosphorylation step as the general base catalyst that abstracts a proton from the 3-hydroxyl group. In this study, the catalytic mechanism of this rare type of decarboxylase is re-investigated by structural and mutagenic studies on the enzyme from a thermoacidophilic archaeon The crystal structures of the archaeal enzyme in complex with ()-5-diphosphomevalonate and adenosine 5'--(3-thio)triphosphate or with ()-5-diphosphomevalonate and ADP are newly solved, and theoretical analysis based on the structure suggests the inability of proton abstraction by the conserved aspartate residue, Asp-281. Site-directed mutagenesis on Asp-281 creates mutants that only show diphosphomevalonate 3-kinase activity, demonstrating that the residue is required in the process of phosphate elimination/decarboxylation, rather than in the preceding phosphorylation step. These results enable discussion of the catalytic roles of the aspartate residue and provide clear proof of the involvement of a long predicted intermediate, ()-3-phospho-5-diphosphomevalonate, in the reaction of the enzyme.

PubMed: 28003359
DOI: 10.1074/jbc.M116.752535

Experimental method

X-RAY DIFFRACTION (1.5 Å)