Molecular mechanism for oxygenation pathway in Rubisco.: Mapping transition structures and intermediates for model compounds of the substrate system

Abstract

Transition structures and molecular intermediates related to the molecular mechanism of the reaction catalyzed by Rubisco have been theoretically characterized for different steps in the dioxygen fixation at the C2 center, hydrolysis and C2–C3 bond breaking. Hydroxypropanone is used as a minimal model for the substrate d-ribulose-1,5-bisphosphate, while ab initio SCF MO calculations at a 6-31G ** basis set level of theory were used. The set of transition structures map out all aspects of the reaction pathway for the real system without reliance on external acidic or basic sidechain residues, these latter may play a key role at a kinetic level not only stabilizing intramolecular transition structures. The present results represent a basic model for a simpler mechanistic alternative.