Structural and Molecular Dynamics Studies of UDP Glucose Pyrophosphorylase Dimerization in Rice (Oryza sativa L.)

UGPase enzyme is involved in sucrose synthesis as a catalyzing agent in the reaction, Mg +2 -UTP + Glu-1-P PPi + UDP-Glu. It catalyzes both forward and reverse reaction depending on the metabolic status of the tissue. UGPase contains three domains: N-terminal domain, catalytic domain with nucleotide binding loop at center and the C-terminal domain. UGPase as a monomer is the functionally active in most photosynthetic plants and microorganisms. Comparative structural modelling of UGPase was performed using models predicted from Modeller, Swiss-Model and I-TASSER. All predicted models were further assessed, evaluated and refined through QMEAN, WHATIF and SAVES server to achieve most stable model. To study the interaction between monomers units’, homodimers were built through protein-protein docking. Hydrogen bonding between monomer units, solvent accessible area and ligand binding/active sites were predicted with H Bond, NACCESS and CastP server. Solvent accessible area in dimer was approx. 100-200 Å smaller as compared to monomer. This study showed that reduction in solvent accessible area and subsequent smaller active site resulted in loss of activity due to dimerization in UGPase.