Transition State Structures and Intermediates Modeling Carboxylation Reactions Catalyzed by Rubisco. A Quantum Chemical Study of the Role of Magnesium and Its Coordination Sphere

Abstract

The reactive sequences mimicking the carboxylation chemistry catalyzed by Rubisco are characterized at HF/3-21G and HF/6-31G** calculation levels. Hydroxypropanone, C1H3−C2O−C3H2OH, represents the substrate D-ribulose-1,5-bisphosphate, while the enzyme active site is modeled with residues found at the coordination sphere of magnesium: a carbamylated ammonia (Lys 201), two formiate (Asp 202 and Glu 204), and one water molecule. Theoretical characterization of saddle points of index one, transition state (T-S) structures, starts with an intramolecular enolization process previously reported, yielding an enediol intermediate (carbonyl oxygen at C2 is transformed into alcohol, C2-OH). The CO2 addition, with a concomitant hydrogen transfer from the C3-OH to carbon dioxide constitutes the second step, with formation of a carboxy-ketone (carboxy-aldehyde in our model) intermediate, C1H3−C2OH(COOH)−C3HO. Adding a water molecule at C3 is the third step, followed by the C2−C3 bond break. This process is coupled with another intramolecular hydrogen transfer, yielding in the real substrate 3-phospho-D-glycerate and an intermediate. A final step involving this intermediate is associated with the C2 inversion with formation of another molecule of 3-phospho-D-glycerate. A detailed comparison of T-Ss with and without inclusion of the residues forming the magnesium coordination sphere is presented. Except for the already reported enolization T-S and also for one of the C2−C3 bond rupture T-Ss, the key geometric elements and the amplitudes of the transition vectors are fairly invariant to the presence of the magnesium coordination sphere. The reported transition structures are joined in order by appropriate precursor and successor complexes reflecting the real chemistry. The present model can hence be related to a sequential ordered kinetics. Most experimental aspects of the reaction pathways catalyzed by this key enzyme find explanation within the molecular mechanism obtained from the present theoretical results.