DFT study of the reaction proceeding in the cytidine deaminase

Kędzierski, Paweł; Sokalski, W. Andrzej; Cheng, Hansong; Mitchell, J. W.; Leszczyński, Jerzy

doi:10.1016/j.cplett.2003.10.042

Cited by 7 publications

(6 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…carried out the most comprehensive theoretical studies of the CDA active site based on a large active site model using the PM3 Hamiltonian[55, 56]. However, the early stage of the reaction mechanism proposed by density functional theory is different from that previously reported using semiempirical methods[57]. The initial structures of the former theoretical models were based upon the crystal structure of the CDA-inhibitor complex 1CTT from the Protein Data Bank.…”

Section: Resultsmentioning

confidence: 99%

QM/MM X-ray refinement of zinc metalloenzymes

Hayik

Merz

2010

Journal of Inorganic Biochemistry

View full text Add to dashboard Cite

Zinc metalloenzymes play an important role in biology. However, due to the limitation of molecular force field energy restraints used in X-ray refinement at medium or low resolutions, the precise geometry of the zinc coordination environment can be difficult to distinguish from ambiguous electron density maps. Due to the difficulties involved in defining accurate force fields for metal ions, the QM/MM (Quantum-Mechanical /Molecular-Mechanical) method provides an attractive and more general alternative for the study and refinement of metalloprotein active sites. Herein we present three examples that indicate that QM/MM based refinement yields a superior description of the crystal structure based on R and R free values and on the inspection of the zinc coordination environment. It is concluded that QM/MM refinement is a useful general tool for the improvement of the metal coordination sphere in metalloenzyme active sites.

show abstract

Section: Resultsmentioning

confidence: 99%

QM/MM X-ray refinement of zinc metalloenzymes

Hayik

Merz

2010

Journal of Inorganic Biochemistry

View full text Add to dashboard Cite

show abstract

“…The enzyme-substrate (ES) complex is in rapid equilibrium with free enzyme and substrate, and k cat solely represents the chemical steps, with the reaction being pH-independent in the neutral pH region (4). The deamination of cytidine by this enzyme has been the subject of several earlier theoretical studies (9)(10)(11)(12)(13)(14)(15), but, despite similarity in the proposed chemical steps, none of these studies has provided energies compatible with the experimental values. A recent study by one of us (16) on the related E. coli cytosine deaminase enzyme yielded a detailed reaction mechanism with very reasonable energetics.…”

Section: Significancementioning

confidence: 87%

Enzyme catalysis by entropy without Circe effect

Kazemi

Himo

Åqvist

2016

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.cytidine deaminase | density functional theory | empirical valence bond method | computational Arrhenius plots M any hypotheses have been put forward to explain the rate acceleration of chemical reactions by enzymes. One of the most influential of these is Jencks' so-called "Circe effect" (1), which posits that the key catalytic effect is associated with substrate binding and that part of the favorable (negative) binding free energy is spent on destabilization of the bound substrate in its ground state. Such ground-state destabilization could, in principle, have different possible physical origins, such as reduction of translational, rotational, and conformational substrate entropies; steric and conformational strain; or electrostatic destabilization and desolvation effects (1). In particular, the entropic explanation enjoys widespread popularity and is often invoked to rationalize the catalytic power of enzymes in terms of proximity and alignment of the reacting groups (2). It is then assumed that part of the substrate-binding free energy is spent on restricting the substrate motions and correctly aligning the substrate for reaction, which implies a negative contribution to the binding entropy. This scenario, in turn, would enable the substrate to climb the activation barrier with a smaller entropy loss than in solution, because the entr...

show abstract

“…This approach has been successfully employed to study the reaction mechanisms of a large number of enzymes, − including many zinc-containing ones. − It should also be pointed out that the reaction mechanisms of several other deaminases have been studied computationally using various techniques. These include, for example, yeast cytosine deaminase ( y CD) from Saccharomyces cerevisiae , − cytidine deaminase from E. coli ( e CDA), − adenosine deaminase (ADA) from Mus musculus , , t RNA-specific adenosine deaminase (TadA) from E. coli , and guanine deaminase from Bacillus subtilis ( b GD) . Some results from these studies will be discussed later when relevant.…”

Section: Introductionmentioning

confidence: 99%

Reaction Mechanism of Zinc-Dependent Cytosine Deaminase fromEscherichia coli: A Quantum-Chemical Study

2014

View full text Add to dashboard Cite

The reaction mechanism of cytosine deaminase from Escherichia coli is studied using density functional theory. This zinc-dependent enzyme catalyzes the deamination of cytosine to form uracil and ammonia. The calculations give a detailed description of the catalytic mechanism and establish the role of important active-site residues. It is shown that Glu217 is essential for the initial deprotonation of the metal-bound water nucleophile and the subsequent protonation of the substrate. It is also demonstrated that His246 is unlikely to function as a proton shuttle in the nucleophile activation step, as previously proposed. The steps that follow are nucleophilic attack by the metal-bound hydroxide, protonation of the leaving group assisted by Asp313, and C-N bond cleavage. The calculated overall barrier is in good agreement with the experimental findings. Finally, the calculations reproduce the experimentally determined inverse solvent deuterium isotope effect, which further corroborates the suggested reaction mechanism.

show abstract

DFT study of the reaction proceeding in the cytidine deaminase

Cited by 7 publications

References 22 publications

QM/MM X-ray refinement of zinc metalloenzymes

QM/MM X-ray refinement of zinc metalloenzymes

Enzyme catalysis by entropy without Circe effect

Reaction Mechanism of Zinc-Dependent Cytosine Deaminase fromEscherichia coli: A Quantum-Chemical Study

Contact Info

Product

Resources

About