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Quantum mechanics/molecular mechanics investigation of the mechanism of phosphate transfer in human uridine-cytidine kinase 2
- Source :
- Organic & Biomolecular Chemistry. 7:2716
- Publication Year :
- 2009
- Publisher :
- Royal Society of Chemistry (RSC), 2009.
-
Abstract
- The mechanisms of enzyme-catalyzed phosphate transfer and hydrolysis reactions are of great interest due to their importance and abundance in biochemistry. The reaction may proceed in a stepwise fashion, with either a pentavalent phosphorane or a metaphosphate anion intermediate, or by a concerted SN2 mechanism. Despite much theoretical work focused on a few key enzymes, a consensus for the mechanism has not been reached, and examples of all three possibilities have been demonstrated. We have investigated the mechanism of human uridine-cytidine kinase 2 (UCK2, EC 2.7.1.48), which catalyzes the transfer of a phosphate group from ATP to the ribose 5'-hydroxyl of cytidine and uridine. UCK2 is normally expressed in human placenta, but is overexpressed in certain cancer cells, where it is responsible for activating a class of antitumor prodrugs. The UCK2 mechanism was investigated by generating a 2D potential energy surface as a function of the P-O bonds forming and breaking, with energies calculated using a quantum mechanics/molecular mechanics potential (B3LYP/6-31G(d):AMBER). The mechanism of phosphate transfer is shown to be concerted, and is accompanied by concerted proton transfer from the 5'-hydroxyl to a conserved active site aspartic acid that serves as a catalytic base. The calculated barrier for this reaction is 15.1 kcal/mol, in relatively good agreement with the experimental barrier of 17.5 kcal/mol. The interactions of the enzyme active site with the reactant, transition state, and product are examined for their implications on the design of anticancer prodrugs or positron emission tomography (PET) reporter probes for this enzyme.
- Subjects :
- Models, Molecular
Stereochemistry
Biochemistry
Molecular mechanics
Article
Catalysis
Phosphates
Uridine kinase
chemistry.chemical_compound
Quantum mechanics
Ribose
Humans
Physical and Theoretical Chemistry
Molecular Structure
biology
Hydrolysis
Organic Chemistry
Active site
Cytidine
Phosphorane
Uridine
chemistry
biology.protein
Quantum Theory
Thermodynamics
SN2 reaction
Uridine Kinase
Subjects
Details
- ISSN :
- 14770539 and 14770520
- Volume :
- 7
- Database :
- OpenAIRE
- Journal :
- Organic & Biomolecular Chemistry
- Accession number :
- edsair.doi.dedup.....3afe22161e86019ad316e1ca60c10fdd