A molecular dynamics exploration of the catalytic mechanism of yeast cytosine deaminase.
Yeast cytosine deaminase (yCD), a zinc metalloenzyme of significant biomedical interest, is investigated by a series of molecular dynamics simulations in its free form and complexed with its reactant (cytosine), product (uracil), several reaction intermediates, and an intermediate analogue. Quantum chemical calculations, used to construct a model for the catalytic Zn ion with its ligands (two cysteines, a histidine, and one water) show, by comparison with crystal structure data, that the cysteines are deprotonated and the histidine is monoprotonated. The simulations suggest that Glu64 plays a critical role in the catalysis by yCD. The rotation of the Glu64 side-chain carboxyl group that can be protonated or deprotonated permits it to act as a proton shuttle between the Zn-bound water and cytosine and subsequent reaction intermediates. Free energy methods are used to obtain the barriers for these rotations, and they are sufficiently small to permit rotation on a nanosecond time scale. In the course of the reaction, cytosine reorients to a geometry to favor nucleophilic attack by a Zn-bound hydroxide. A stable position for a reaction product, ammonia, was located in the active site, and the free energy of exchange with a water molecule was evaluated. The simulations also reveal small motions of the C-terminus and the loop that contains Phe114 that may be important for reactant binding and product release.
Yao
Lishan
L
Department of Chemistry, MSU Center for Biological Modeling, Michigan State University, East Lansing, Michigan 48824, USA.
Sklenak
Stepan
S
Yan
Honggao
H
Cukier
Robert I
RI
D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D003596:Cytosine / Q000737:chemistry; D043525:Cytosine Deaminase / Q000737:chemistry*; D005656:Fungal Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation; D010649:Phenylalanine / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry; D015003:Yeasts / Q000201:enzymology
D005656:Fungal Proteins; D014867:Water; D010649:Phenylalanine; D003596:Cytosine; D043525:Cytosine Deaminase