Quantum Chemical Analysis of the Enolization of Ribulose Bisphosphate:  The First Hurdle in the Fixation of CO₂ by Rubisco

Abstract

A study, using ab initio quantum chemical methods, of the first step in the reaction mechanism of Rubisco, the enolization of the substrate, ribulose bisphosphate, is reported. This is the first such study that takes into account the likely roles of critical features within the active site. On the basis of molecular dynamics relaxation of the complex between activated enzyme and substrate using X-ray crystallographic structures as starting coordinates, a 29-atom fragment that mimicked the active site was constructed. States along a proposed reaction pathway were calculated using density functional theory and Moller-Plesset second-order perturbation theory. The results are consistent with the postulate that the base that abstracts the C3 proton of ribulose bisphosphate is the metal-stabilized carbamate of Lys-201 formed during the activation process. The calculations suggest that the active-site residue, Lys-175, is charged before enolization commences and they indicate a possible means by which the enzyme directs the incoming CO2 to attack the C2 carbon atom of the enediol, rather than the chemically very similar C3 atom.

Structure and function of Rubisco

“…refs. [51,64,105]). While these calculations differed in certain details, they consistently identified the carbamylated Lys201 as a key player in catalysis.…”

“…This is likely to result in shifts of the position of individual residues in the active site. In particular Thr173, which interacts with the C2-hydroxyl of 2CABP, or Lys175, which has been suggested play a dual role in catalysis as an acid, as a base, or both [15,51,64,107], see above, are likely to be influenced. Perhaps more importantly, the shift in main-chain residues is likely to influence dynamics of the active site, thereby affecting catalysis.…”

Fixation of Carbon Dioxide by Oxalic Amidinato Magnesium Complexes: Structures and Reactions of Trimetallic Magnesium Carbamato and Related Complexes

“…The resulting enol reacts with carbon dioxide in the coordination sphere of the magnesium centre to form a new C-C bond (for reviews see refs. [9][10][11] ). The structure of various forms of Rubisco have been elucidated by X-ray crystallography.…”

Multifaceted Roles of Lys166 of Ribulose-bisphosphate Carboxylase/Oxygenase As Discerned by Product Analysis and Chemical Rescue of Site-Directed Mutants

“…Although the unusually strong nucleophilicity and high acidity of Lys166 (pK a of 7.9) (43) suggest that it functions as a general base, its -amino nitrogen is 6.5 Å from C3 but only 3.1 Å from O2 of bound RuBP (12). If the -amino group is protonated within this complex, as deduced from quantum chemical analysis (17), it is ideally positioned to facilitate abstraction of the C3 proton by the carbamate via polarization of the C2 carbonyl group as emphasized in this same study. Thus, the troubling conflicts between functional and structural studies will have been resolved.…”