ArticleJournal of the American Chemical Society2015
Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase.
Article in Journal of the American Chemical Society, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed, 39 citations in OpenAlex.
- Towards an enzyme cascade synthesis of the bulk chemical acrylic acid.Nature communications · 2026Article
- Structural insights into urocanate reductase using room-temperature X-ray crystallography.Acta crystallographica. Section D, Structural biology · 2026Article
- The Role of Protein Side Chains in Enzyme-Activating Conformational Changes: Lessons from Studies on Variant Enzymes.Chemical reviews · 2025Review
- Enzyme Architecture: Activation of Phosphite Dehydrogenase-Catalyzed Hydride Transfer by NADBiochemistry · 2025Article
- Glycerol 3-Phosphate Dehydrogenase Catalyzed Hydride Transfer: Enzyme Activation by Cofactor Pieces.Biochemistry · 2024Article
- Triosephosphate Isomerase: The Crippling Effect of the P168A/I172A Substitution at the Heart of an Enzyme Active Site.Biochemistry · 2023Article
- Utilization of Cofactor Binding Energy for Enzyme Catalysis: Formate Dehydrogenase-Catalyzed Reactions of the Whole NAD Cofactor and Cofactor Pieces.Biochemistry · 2023Article
- The Role of Asn11 in Catalysis by Triosephosphate Isomerase.Biochemistry · 2023Article
- Kinetics and mechanism for enzyme-catalyzed reactions of substrate pieces.Methods in enzymology · 2023Article
- Adenylate Kinase-Catalyzed Reactions of AMP in Pieces: Specificity for Catalysis at the Nucleoside Activator and Dianion Catalytic Sites.Biochemistry · 2022Article
- Identification and Mutation Analysis of Nonconserved Residues on the TIM-Barrel Surface of GH5_5 Cellulases for Catalytic Efficiency and Stability Improvement.Applied and environmental microbiology · 2022Article
- Enabling Role of Ligand-Driven Conformational Changes in Enzyme Evolution.Biochemistry · 2022Review
- Protein-Ribofuranosyl Interactions Activate Orotidine 5'-Monophosphate Decarboxylase for Catalysis.Biochemistry · 2021Article
- Neutron structures ofIUCrJ · 2021Article
- Linear Free Energy Relationships for Enzymatic Reactions: Fresh Insight from a Venerable Probe.Accounts of chemical research · 2021Review
- Phosphodianion Activation of Enzymes for Catalysis of Central Metabolic Reactions.Journal of the American Chemical Society · 2021Article
- The role of ligand-gated conformational changes in enzyme catalysis.Biochemical Society transactions · 2019Review
- Uncovering the Role of Key Active-Site Side Chains in Catalysis: An Extended Brønsted Relationship for Substrate Deprotonation Catalyzed by Wild-Type and Variants of Triosephosphate Isomerase.Journal of the American Chemical Society · 2019Article
- Missense variant in TPI1 (Arg189Gln) causes neurologic deficits through structural changes in the triosephosphate isomerase catalytic site and reduced enzyme levels in vivo.Biochimica et biophysica acta. Molecular basis of disease · 2019Article
- Protein Flexibility and Stiffness Enable Efficient Enzymatic Catalysis.Journal of the American Chemical Society · 2019Article
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3 authors at 1 institution in 1 country.
Funding
Abstract
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 [(k(cat)/K(m))(GAP) and (k(cat)/K(m))DHAP] and of the substrate pieces glycolaldehyde and phosphite dianion (k(cat)/K(HPi)K(GA)) 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 k(cat) for isomerization of GAP and K(d)(⧧) 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.
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