Role of each residue in catalysis in the active site of pyrimidine nucleoside phosphorylase from Bacillus subtilis: a hybrid QM/MM study.
Pyrimidine nucleoside phosphorylase (PYNP) catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway. We have built a model of a closed active conformation of the three-dimensional structure of PYNP from Bacillus subtilis. Using docking, molecular dynamics, and hybrid quantum-mechanical/molecular-mechanical methods to study the reaction mechanics between PYNP and a substrate, we identified the role of each residue in the active site during the entire catalytic process. The results indicate that the function of His(82), Arg(169), and Lys(188) is to stabilize the uridine in a high-energy conformation by means of electrostatic interactions and that these residues are involved in catalysis. In addition, the function of Asp(162) is likely to activate Lys(188) for phosphorolytic catalysis through polarization effects.
State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, PR China.
Xue-Feng
XF
Gao
Xu-Ri
XR
Huang
Chia-Chung
CC
Sun
D000596:Amino Acids / Q000737:chemistry*; D001412:Bacillus subtilis / Q000201:enzymology*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002384:Catalysis; D008956:Models, Chemical; D008958:Models, Molecular; D010430:Pentosyltransferases / Q000737:chemistry* / Q000378:metabolism; D017433:Protein Structure, Secondary; D057845:Pyrimidine Phosphorylases; D011789:Quantum Theory; D014529:Uridine / Q000737:chemistry / Q000378:metabolism
D000596:Amino Acids; D001426:Bacterial Proteins; D010430:Pentosyltransferases; D057845:Pyrimidine Phosphorylases; D014529:Uridine