Main content area

Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase

Zhai, Xiang, Amyes, Tina L., Richard, John P.
Journal of the American Chemical Society 2015 v.137 no.48 pp. 15185-15197
active sites, amides, catalysts, catalytic activity, energy, enzyme substrates, hydrogen bonding, isomerization, mutants, mutation, phosphates, triose-phosphate isomerase
The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme–substrate complex. The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G, S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde 3-phosphate [(kcₐₜ/Kₘ)GAP and (kcₐₜ/Kₘ)DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (kcₐₜ/KHPᵢKGA) are reported. The linear logarithmic correlation between these kinetic parameters, with slope of 1.04 ± 0.03, shows that most mutations of TIM result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The second linear logarithmic correlation [slope = 0.53 ± 0.16] between kcₐₜ for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition state for wildtype and many mutant TIM-catalyzed reactions of substrate pieces shows that ca. 50% of the wildtype TIM dianion binding energy, eliminated by these mutations, is expressed at the wildtype Michaelis complex, and ca. 50% is only expressed at the wildtype transition state. Negative deviations from this correlation are observed when the mutation results in a decrease in enzyme reactivity at the catalytic site. The main effect of Y208T, Y208S, and Y208A mutations is to cause a reduction in the total intrinsic dianion binding energy, but the effect of Y208F extends to the catalytic site.