Atomistic details of effect of disulfide bond reduction on active site of Phytase B from Aspergillus niger: A MD Study

The molecular integrity of the active site of phytases from fungi is critical for maintaining phytase function as efficient catalyticmachines. In this study, the molecular dynamics (MD) of two monomers of phytase B from Aspergillus niger, the disulfide intactmonomer (NAP) and a monomer with broken disulfide bonds (RAP), were simulated to explore the conformational basis of theloss of catalytic activity when disulfide bonds are broken. The simulations indicated that the overall secondary and tertiarystructures of the two monomers were nearly identical but differed in some crucial secondary–structural elements in the vicinity ofthe disulfide bonds and catalytic site. Disulfide bonds stabilize the β-sheet that contains residue Arg66 of the active site anddestabilize the α-helix that contains the catalytic residue Asp319. This stabilization and destabilization lead to changes in the shapeof the active–site pocket. Functionally important hydrogen bonds and atomic fluctuations in the catalytic pocket change during theRAP simulation. None of the disulfide bonds are in or near the catalytic pocket but are most likely essential for maintaining thenative conformation of the catalytic site.

Abbreviations

PhyB - 2.5 pH acid phophatese from Aspergillus niger, NAP - disulphide intact monomer of Phytase B, RAP - disulphide reduced monomer of Phytase B, Rg - radius of gyration, RMSD - root mean square deviation, MD - molecular dynamics.