A proficient enzyme

Insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations

Simone Raugei, Michele Cascella, Paolo Carloni

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Decarboxylation of orotidine 5′-monophosphate (Omp) to uridine 5′-monophosphate by orotidine 5′-monophosphate decarboxylase (ODCase) is currently the object of vivid debate. Here, we clarify its enzymatic activity with long time scale classical molecular dynamics and hybrid ab initio Car-Parrinello/ molecular mechanics simulations. The lack of structural (experimental) information on the ground state of ODCase/Omp complex is overcome by a careful construction of the model and the analysis of three different strains of the enzyme. We find that the ODCase/substrate complex is characterized by a very stable charged network Omp-Lys-Asp-Lys-Asp, which is incompatible with the previously proposed direct decarboxylation driven by a ground-state destabilization. A direct decarboxylation induced by a transition-state electrostatic stabilization is consistent with our findings. The calculated activation free energy for the direct decarboxylation with the formation of a C6 carboanionic intermediate yields an overall rate enhancement by the enzyme (kcat/Kwat = 3.5 × 1016) in agreement with experiments (kcat/kwat = 1.7 × 1017). The decarboxylation is accompanied by the movement of a fully conserved lysine residue toward the developing negative charge at the C6 position.

Original languageEnglish
Pages (from-to)15730-15737
Number of pages8
JournalJournal of the American Chemical Society
Volume126
Issue number48
Publication statusPublished - Dec 8 2004

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Decarboxylation
Carboxy-Lyases
Computer Simulation
Enzymes
Computer simulation
Ground state
Uridine Monophosphate
Molecular mechanics
Molecular Dynamics Simulation
Mechanics
Static Electricity
Free energy
Lysine
Molecular dynamics
Electrostatics
Railroad cars
Stabilization
Chemical activation
orotidine
orotidylic acid

ASJC Scopus subject areas

  • Chemistry(all)

Cite this

A proficient enzyme : Insights on the mechanism of orotidine monophosphate decarboxylase from computer simulations. / Raugei, Simone; Cascella, Michele; Carloni, Paolo.

In: Journal of the American Chemical Society, Vol. 126, No. 48, 08.12.2004, p. 15730-15737.

Research output: Contribution to journalArticle

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