7TIM

STRUCTURE OF THE TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX: AN ANALOGUE OF THE INTERMEDIATE ON THE REACTION PATHWAY

Summary for 7TIM

• Entry DOI: 10.2210/pdb7tim/pdb
• Descriptor: TRIOSEPHOSPHATE ISOMERASE, PHOSPHOGLYCOLOHYDROXAMIC ACID (3 entities in total)
• Functional Keywords: intramolecular oxidoreductase
• Biological source: Saccharomyces cerevisiae (baker's yeast)
• Total number of polymer chains: 2
• Total formula weight: 53734.54

Authors

Davenport, R.C.,Bash, P.A.,Seaton, B.A.,Karplus, M.,Petsko, G.A.,Ringe, D. (deposition date: 1991-04-23, release date: 1993-10-31, Last modification date: 2024-02-28)

Primary citation

Davenport, R.C.,Bash, P.A.,Seaton, B.A.,Karplus, M.,Petsko, G.A.,Ringe, D.
Structure of the triosephosphate isomerase-phosphoglycolohydroxamate complex: an analogue of the intermediate on the reaction pathway.
Biochemistry, 30:5821-5826, 1991

PubMed Abstract: The glycolytic enzyme triosephosphate isomerase (TIM) catalyzes the interconversion of the three-carbon sugars dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde 3-phosphate (GAP) at a rate limited by the diffusion of substrate to the enzyme. We have solved the three-dimensional structure of TIM complexed with a reactive intermediate analogue, phosphoglycolohydroxamate (PGH), at 1.9-A resolution and have refined the structure to an R-factor of 18%. Analysis of the refined structure reveals the geometry of the active-site residues and the interactions they make with the inhibitor and, by analogy, the substrates. The structure is consistent with an acid-base mechanism in which the carboxylate of Glu-165 abstracts a proton from carbon while His-95 donates a proton to oxygen to form an enediol (or enediolate) intermediate. The conformation of the bound substrate stereoelectronically favors proton transfer from substrate carbon to the syn orbital of Glu-165. The crystal structure suggests that His-95 is neutral rather than cationic in the ground state and therefore would have to function as an imidazole acid instead of the usual imidazolium. Lys-12 is oriented so as to polarize the substrate oxygens by hydrogen bonding and/or electrostatic interaction, providing stabilization for the charged transition state. Asn-10 may play a similar role.

PubMed: 2043623
DOI: 10.1021/bi00238a002

Experimental method

X-RAY DIFFRACTION (1.9 Å)