ArticleJournal of the American Chemical Society2013
Substrate distortion contributes to the catalysis of orotidine 5'-monophosphate decarboxylase.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 30 citations in OpenAlex.
- Dynamically Interacting Protein Networks Provide a Mechanism to Overcome the Enormous Intrinsic Barrier to Orotidine 5'-Monophosphate Decarboxylation.ACS central science · 2025Article
- Identification of Scaffold Specific Energy Transfer Networks in the Enthalpic Activation of Orotidine 5'-Monophosphate Decarboxylase.bioRxiv : the preprint server for biology · 2025Article
- Developing nucleoside tailoring strategies against SARS-CoV-2 via ribonuclease targeting chimera.Science advances · 2024Article
- Unravelling Enzymatic Features in a Supramolecular Iridium Catalyst by Computational Calculations.Chemistry (Weinheim an der Bergstrasse, Germany) · 2022Article
- Structural basis for antibiotic action of the BNature chemical biology · 2020Article
- How the Destabilization of a Reaction Intermediate Affects Enzymatic Efficiency: The Case of Human Transketolase.ACS catalysis · 2020Article
- Role of the Carboxylate in Enzyme-Catalyzed Decarboxylation of Orotidine 5'-Monophosphate: Transition State Stabilization Dominates Over Ground State Destabilization.Journal of the American Chemical Society · 2019Article
- Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.Acta crystallographica. Section F, Structural biology communications · 2018Article
- Orotidine 5'-Monophosphate Decarboxylase: Probing the Limits of the Possible for Enzyme Catalysis.Accounts of chemical research · 2018Review
- Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase.Journal of the American Chemical Society · 2016Article
- Mathematical and computational modeling in biology at multiple scales.Theoretical biology & medical modelling · 2014Review
- Investigating the role of a backbone to substrate hydrogen bond in OMP decarboxylase using a site-specific amide to ester substitution.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Orotidine 5'-monophosphate decarboxylase (ODCase) accelerates the decarboxylation of orotidine 5'-monophosphate (OMP) to uridine 5'-monophosphate (UMP) by 17 orders of magnitude. Eight new crystal structures with ligand analogues combined with computational analyses of the enzyme's short-lived intermediates and the intrinsic electronic energies to distort the substrate and other ligands improve our understanding of the still controversially discussed reaction mechanism. In their respective complexes, 6-methyl-UMP displays significant distortion of its methyl substituent bond, 6-amino-UMP shows the competition between the K72 and C6 substituents for a position close to D70, and the methyl and ethyl esters of OMP both induce rotation of the carboxylate group substituent out of the plane of the pyrimidine ring. Molecular dynamics and quantum mechanics/molecular mechanics computations of the enzyme-substrate complex also show the bond between the carboxylate group and the pyrimidine ring to be distorted, with the distortion contributing a 10-15% decrease of the ΔΔG(⧧) value. These results are consistent with ODCase using both substrate distortion and transition-state stabilization, primarily exerted by K72, in its catalysis of the OMP decarboxylation reaction.
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Registered trials
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.