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Enzyme architecture: remarkably similar transition states for triosephosphate isomerase-catalyzed reactions of the whole substrate and the substrate in pieces.

ABSTRACT: Values of (k(cat)/K(m))GAP for triosephosphate isomerase-catalyzed reactions of (R)-glyceraldehyde 3-phosphate and k(cat)/K(HPi)K(GA) for reactions of the substrate pieces glycolaldehyde and HPO3(2-) have been determined for wild-type and the following TIM mutants: I172V, I172A, L232A, and P168A (TIM from Trypanosoma brucei brucei); a 208-TGAG for 208-YGGS loop 7 replacement mutant (L7RM, TIM from chicken muscle); and, Y208T, Y208S, Y208A, Y208F and S211A (yeast TIM). A superb linear logarithmic correlation, with slope of 1.04 ± 0.03, is observed between the kinetic parameters for wild-type and most mutant enzymes, with positive deviations for L232A and L7RM. The unit slope shows that most mutations result in an identical change in the activation barriers for the catalyzed reactions of whole substrate and substrate pieces, so that the two transition states are stabilized by similar interactions with the protein catalyst. This is consistent with a role for dianions as active spectators, which hold TIM in a catalytically active caged form.

SUBMITTER: Zhai X

PROVIDER: S-EPMC3985921 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature

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Enzyme architecture: remarkably similar transition states for triosephosphate isomerase-catalyzed reactions of the whole substrate and the substrate in pieces.

Zhai Xiang X Amyes Tina L TL Richard John P JP

Journal of the American Chemical Society 20140306 11

Values of (k(cat)/K(m))GAP for triosephosphate isomerase-catalyzed reactions of (R)-glyceraldehyde 3-phosphate and k(cat)/K(HPi)K(GA) for reactions of the substrate pieces glycolaldehyde and HPO3(2-) have been determined for wild-type and the following TIM mutants: I172V, I172A, L232A, and P168A (TIM from Trypanosoma brucei brucei); a 208-TGAG for 208-YGGS loop 7 replacement mutant (L7RM, TIM from chicken muscle); and, Y208T, Y208S, Y208A, Y208F and S211A (yeast TIM). A superb linear logarithmic ...[more]

PMID: 24588650

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Project description:Two mutations of the phosphodianion gripper loop in chicken muscle triosephosphate isomerase (cTIM) were examined: (1) the loop deletion mutant (LDM) formed by removal of residues 170-173 [Pompliano, D. L., et al. (1990) Biochemistry 29, 3186-3194] and (2) the loop 6 replacement mutant (L6RM), in which the N-terminal hinge sequence of TIM from eukaryotes, 166-PXW-168 (X = L or V), is replaced by the sequence from archaea, 166-PPE-168. The X-ray crystal structure of the L6RM shows a large displacement of the side chain of E168 from that for W168 in wild-type cTIM. Solution nuclear magnetic resonance data show that the L6RM results in significant chemical shift changes in loop 6 and surrounding regions, and that the binding of glycerol 3-phosphate (G3P) results in chemical shift changes for nuclei at the active site of the L6RM that are smaller than those of wild-type cTIM. Interactions with loop 6 of the L6RM stabilize the enediolate intermediate toward the elimination reaction catalyzed by the LDM. The LDM and L6RM result in 800000- and 23000-fold decreases, respectively, in kcat/Km for isomerization of GAP. Saturation of the LDM, but not the L6RM, by substrate and inhibitor phosphoglycolate is detected by steady-state kinetic analyses. We propose, on the basis of a comparison of X-ray crystal structures for wild-type TIM and the L6RM, that ligands bind weakly to the L6RM because a large fraction of the ligand binding energy is utilized to overcome destabilizing electrostatic interactions between the side chains of E168 and E129 that are predicted to develop in the loop-closed enzyme. Similar normalized yields of DHAP, d-DHAP, and d-GAP are formed in LDM- and L6RM-catalyzed reactions of GAP in D2O. The smaller normalized 12-13% yield of DHAP and d-DHAP observed for the mutant cTIM-catalyzed reactions compared with the 79% yield of these products for wild-type cTIM suggests that these mutations impair the transfer of a proton from O-2 to O-1 at the initial enediolate phosphate intermediate. No products are detected for the LDM-catalyzed isomerization reactions in D2O of [1-(13)C]GA and HPi, but the L6RM-catalyzed reaction in the presence of 0.020 M dianion gives a 2% yield of the isomerization product [2-(13)C,2-(2)H]GA.

Project description:We report that the K12G mutation in triosephosphate isomerase (TIM) from Saccharomyces cerevisiae results in (1) a approximately 50-fold increase in K(m) for the substrate glyceraldehyde 3-phosphate (GAP) and a 60-fold increase in K(i) for competitive inhibition by the intermediate analogue 2-phosphoglycolate, resulting from the loss of stabilizing ground state interactions between the alkylammonium side chain of Lys-12 and the ligand phosphodianion group; (2) a 12000-fold decrease in k(cat) for isomerization of GAP, suggesting a tightening of interactions between the side chain of Lys-12 and the substrate on proceeding from the Michaelis complex to the transition state; and (3) a 6 x 10(5)-fold decrease in k(cat)/K(m), corresponding to a total 7.8 kcal/mol stabilization of the transition state by the cationic side chain of Lys-12. The yields of the four products of the K12G TIM-catalyzed isomerization of GAP in D(2)O were quantified as dihydroxyacetone phosphate (DHAP) (27%), [1(R)-(2)H]DHAP (23%), [2(R)-(2)H]GAP (31%), and methylglyoxal (18%) from an enzyme-catalyzed elimination reaction. The K12G mutation has only a small effect on the relative yields of the three products of the transfer of a proton to the TIM-bound enediol(ate) intermediate in D(2)O, but it strongly favors catalysis of the elimination reaction to give methylglyoxal. The K12G mutation also results in a >or=14-fold decrease in k(cat)/K(m) for isomerization of bound glycolaldehyde (GA), although the dominant observed product of the mutant enzyme-catalyzed reaction of [1-(13)C]GA in D(2)O is [1-(13)C,2,2-di-(2)H]GA from a nonspecific protein-catalyzed reaction. The observation that the K12G mutation results in a large decrease in k(cat)/K(m) for the reactions of both GAP and the neutral truncated substrate [1-(13)C]GA provides evidence for a stabilizing interaction between the cationic side chain of Lys-12 and the negative charge that develops at the enolate-like oxygen in the transition state for deprotonation of the sugar substrate "piece".

Dataset Information

Enzyme architecture: remarkably similar transition states for triosephosphate isomerase-catalyzed reactions of the whole substrate and the substrate in pieces.

Publications

Enzyme architecture: remarkably similar transition states for triosephosphate isomerase-catalyzed reactions of the whole substrate and the substrate in pieces.

Similar Datasets

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