Quantum-based modeling implies that bidentate Arg⁸⁹-substrate binding enhances serine/threonine protein...

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Protein phosphatase 2A (PP2A) holoenzymes are crucial for regulating protein phosphorylation.
• PP2A comprises scaffold (A), catalytic (C), and regulatory (B) subunits.
• The catalytic mechanism involves a bimetal system and a conserved core sequence.

Purpose of the Study:

• To investigate the role of arginine-89 (Arg89) in the catalytic hydrolysis of PP2A.
• To determine if Arg89 directly binds the substrate's phosphate group during hydrolysis.
• To understand the implications of Arg89's interaction with regulatory subunits for PP2A function and disease.

Main Methods:

• Quantum-based hybrid [ONIOM(UB3LYP/6-31G(d):UPM7)] calculations were performed.
• 39-residue models of the PP2A(PPP2R5D)/phosphoserine system were used.
• Activation barriers for hydrolysis were estimated with and without direct Arg89-substrate binding.

Main Results:

• Solvation-corrected activation barriers were calculated: ΔH‡ ≈ ΔE‡ = +15.5 kcal/mol (direct binding) vs. +18.8 kcal/mol (indirect binding).
• Direct bidentate Arg89-substrate binding significantly lowers the activation barrier for hydrolysis.
• Arg89's interaction with B:Glu198 in PP2A(PPP2R5D) may sequester its catalytic function.

Conclusions:

• Bidentate Arg89-substrate binding is critical for optimal PP2A catalytic activity.
• The pathogenic E198K variant of B56δ may alter PP2A function by changing the charge at this interface.
• PP2A(PPP2R5D) activity is likely suppressed under native conditions by the B:Glu198 interaction with C:Arg89.