ArticleBiochemistry2012
Induced fit and the catalytic mechanism of isocitrate dehydrogenase.
Article in Biochemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
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- Metal coordination and enzymatic reaction of the glioma-target R132H isocitrate dehydrogenase 1: Insights by molecular simulations.PloS one · 2025Article
- Molecular insights and functional analysis of isocitrate dehydrogenase in two gram-negative pathogenic bacteria.World journal of microbiology & biotechnology · 2024Article
- Tartrate Dehydrogenase in Bacillus Species: Deciphering Unique Catalytic Diversity Through Kinetic, Structural and Molecular Docking Analysis.The protein journal · 2024Article
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- A CRISPRi mediated self-inducible system for dynamic regulation of TCA cycle and improvement of itaconic acid production inSynthetic and systems biotechnology · 2022Article
- 6-Phosphogluconate dehydrogenase and its crystal structures.Acta crystallographica. Section F, Structural biology communications · 2022Review
- Biochemical Characterization of Recombinant Isocitrate Dehydrogenase and Its Putative Role in the Physiology of an Acidophilic Micrarchaeon.Microorganisms · 2021Article
- FATCAT 2.0: towards a better understanding of the structural diversity of proteins.Nucleic acids research · 2020Article
- Molecular basis for the function of the αβ heterodimer of human NAD-dependent isocitrate dehydrogenase.The Journal of biological chemistry · 2019Article
- Proteomic profiling of3 Biotech · 2019Article
- Adaptive Landscapes in the Age of Synthetic Biology.Molecular biology and evolution · 2019Review
- Crystal structure of Arabidopsis thaliana glutamyl-tRNAPhotosynthesis research · 2018Article
- Characterizing Lysine Acetylation of Isocitrate Dehydrogenase in Escherichia coli.Journal of molecular biology · 2018Article
- Crystal Structures of the Putative Isocitrate Dehydrogenase fromArchaea (Vancouver, B.C.) · 2018Article
- Escherichia coli D-malate dehydrogenase, a generalist enzyme active in the leucine biosynthesis pathway.The Journal of biological chemistry · 2014Article
- Evolution of a transition state: role of Lys100 in the active site of isocitrate dehydrogenase.Chembiochem : a European journal of chemical biology · 2014Article
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
NADP(+) dependent isocitrate dehydrogenase (IDH; EC 1.1.1.42) belongs to a large family of α-hydroxyacid oxidative β-decarboxylases that catalyze similar three-step reactions, with dehydrogenation to an oxaloacid intermediate preceding β-decarboxylation to an enol intermediate followed by tautomerization to the final α-ketone product. A comprehensive view of the induced fit needed for catalysis is revealed on comparing the first "fully closed" crystal structures of a pseudo-Michaelis complex of wild-type Escherichia coli IDH (EcoIDH) and the "fully closed" reaction product complex of the K100M mutant with previously obtained "quasi-closed" and "open" conformations. Conserved catalytic residues, binding the nicotinamide ring of NADP(+) and the metal-bound substrate, move as rigid bodies during domain closure by a hinge motion that spans the central β-sheet in each monomer. Interactions established between Thr105 and Ser113, which flank the "phosphorylation loop", and the nicotinamide mononucleotide moiety of NADP(+) establish productive coenzyme binding. Electrostatic interactions of a Lys100-Leu103-Asn115-Glu336 tetrad play a pivotal role in assembling a catalytically competent active site. As predicted, Lys230* is positioned to deprotonate/reprotonate the α-hydroxyl in both reaction steps and Tyr160 moves into position to protonate C3 following β-decarboxylation. A proton relay from the catalytic triad Tyr160-Asp307-Lys230* connects the α-hydroxyl of isocitrate to the bulk solvent to complete the picture of the catalytic mechanism.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.