Stabilization of a transition-state analogue at the active site of yeast cytosine deaminase: importance of proton transfers.
It is believed that the binding of pyrimidin-2-one to cytosine deaminase (CD) leads to the formation of 4-[R]-hydroxyl-3,4-dihydropyrimidine (DHP). Here the formation of transition-state analogue (TSA) at the active site of yeast cytosine deaminase (yCD) is investigated by quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) and free energy simulations. It is shown that DHP may in fact be unstable in the active site and a proton transfer from the Zn hydroxide group to Glu-64 may occur during the nucleophilic attack, leading to an alkoxide-like TSA complex instead. The free energy simulations for the nucleophilic attack process show that the proton transfer from the Zn hydroxide to Glu-64 may play an important role in stabilizing the TSA complex.
Xu
Qin
Q
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA.
Guo
Haobo
H
Gorin
Andrey
A
Guo
Hong
H
D001665:Binding Sites; D002384:Catalysis; D003198:Computer Simulation; D043525:Cytosine Deaminase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D018698:Glutamic Acid / Q000737:chemistry* / Q000378:metabolism; D006878:Hydroxides / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D015394:Molecular Structure; D011487:Protein Conformation; D011522:Protons; D011741:Pyrimidine Nucleosides / Q000737:chemistry* / Q000378:metabolism; D011789:Quantum Theory; D012441:Saccharomyces cerevisiae / Q000201:enzymology*; D013816:Thermodynamics; D017967:Zinc Compounds / Q000737:chemistry* / Q000378:metabolism
D006878:Hydroxides; D011522:Protons; D011741:Pyrimidine Nucleosides; D017967:Zinc Compounds; D018698:Glutamic Acid; D043525:Cytosine Deaminase; C052745:zinc hydroxide