Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism

doi:10.1073/pnas.141230998

Substrate conformational transitions in the active site of chorismate mutase: Their role in the catalytic mechanism

^*Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138; and ^†Laboratoire de Chimie Biophysique, Institut Le Bel, Université Louis Pasteur, 67000 Strasbourg, France

Contributed by William N. Lipscomb

Abstract

Chorismate mutase acts at the first branch-point of aromatic amino acid biosynthesis and catalyzes the conversion of chorismate to prephenate. The results of molecular dynamics simulations of the substrate in solution and in the active site of chorismate mutase are reported. Two nonreactive conformers of chorismate are found to be more stable than the reactive pseudodiaxial chair conformer in solution. It is shown by QM/MM molecular dynamics simulations, which take into account the motions of the enzyme, that when these inactive conformers are bound to the active site, they are rapidly converted to the reactive chair conformer. This result suggests that one contribution of the enzyme is to bind the more prevalent nonreactive conformers and transform them into the active form in a step before the chemical reaction. The motion of the reactive chair conformer in the active site calculated by using the QM/MM potential generates transient structures that are closer to the transition state than is the stable CHAIR conformer.

Footnotes

↵ ‡ To whom reprint requests should be addressed. E-mail: marci{at}tammy.harvard.edu.
Abbreviations:

CM,

chorismate mutase;

YCM,

yeast CM;

TSA,

transition-state analogue;

CHAIR,

chair pseudodiaxial conformer;

DIAX,

a pseudodiaxial conformer;

DIEQ1,

a pseudodiequatorial conformer;

DIEQ2,

the lowest energy conformation of chorismate in the gas phase;

ex-DIAX,

an extended pseudodiaxial conformer;

SCC-DFTB,

the self-consistent charge density functional tight-binding method;

QM/MM,

quantum-mechanical/molecular mechanical