Transition state structures and intermediates modeling carboxylation reactions catalyzed by rubisco. a quantum chemical study of the role of magnesium and its coordination sphere

The reactive sequences mimicking the carboxylation chemistry catalyzed by R ubisco are characterized at HF/3-21G and HF/6-31G** calculation levels. Hyd roxypropanone, (CH3)-H-1-(CO)-O-2-(CH2OH)-H-3, represents the substrate D-r ibulose-1,5-bisphosphate, while the enzyme active site is modeled with resi dues found at the coordination sphere of magnesium: a carbamylated ammonia (Lys 201), two formiate (Asp 202 and Glu 204), and one water molecule. Theo retical characterization of saddle points of index one, transition state (T -S) structures, starts with an intramolecular enolization process previousl y reported, yielding an enediol intermediate (carbonyl oxygen at C-2 is tra nsformed into alcohol, C-2-OH). The CO2 addition, with a concomitant hydrog en transfer from the C-3-OH to carbon dioxide constitutes the second step, with formation of a carboxy-ketone (carboxy-aldehyde in our model) intermed iate, (CH3)-H-1-(COH)-O-2(COOH)-(CHO)-H-3. Adding a water molecule at C-3 i s the third step, followed by the C-2-C-3 bond break. This process is coupl ed with another intramolecular hydrogen transfer, yielding in the real subs trate 3-phospho-D-glycerate and an intermediate. A final step involving thi s intermediate is associated with the C-2 inversion with formation of anoth er molecule of 3-phospho-D-glycerate. A detailed comparison of T-Ss with an d without inclusion of the residues forming the magnesium coordination sphe re is presented. Except for the already reported enolization T-S and also f or one of the C-2-C-3 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 ar e joined in order by appropriate precursor and successor complexes reflecti ng the real chemistry. The present model can hence be related to a sequenti al ordered kinetics, Most experimental aspects of the reaction pathways cat alyzed by this key enzyme find explanation within the molecular mechanism o btained from the present theoretical results.