Quantum-Based Modeling of Dephosphorylation in the Catalytic Site of Serine/Threonine Protein Phosphatase-5 (PPP5C)

E Alan Salter,Andrzej Wierzbicki,Richard E Honkanen

doi:10.3390/catal10060674

E Alan Salter, Andrzej Wierzbicki + Show 1 more

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https://doi.org/10.3390/catal10060674

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Journal: Catalysts (Basel, Switzerland)	Publication Date: Jun 16, 2020
Citations: 4	License type: CC BY 4.0

Affiliation: University of South Alabama

Abstract

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M1/M2), an associated bridge hydroxide (W1(OH−)), an M1-bound water/hydroxide (W2), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W1(OH−) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W1(OH−) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His304/Asp274 tandem, with W2 assigned as a water molecule: W2(H2O). Arg275, proximal to M1, stabilizes the substrate and TS by binding both the ester oxygen (Oγ) and a phosphoryl oxygen (O1) in a bidentate fashion; in the product state, Tyr451 aids in decoupling Arg275 from O1 of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg275 is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg275 plays during the hydroxide attack was not correctly accounted for.

Highlights

Protein phosphorylation increases the functional diversity of the proteome and is critical to the regulation of numerous cellular processes
The hydroxyl groups of serine, threonine, and tyrosine are amenable to phosphoryl attachment via Catalysts 2020, 10, 674; doi:10.3390/catal10060674
Our interest is the common mechanism by which the members of the phosphoprotein Our interest is the common mechanism by which the members of the phosphoprotein phosphatase phosphatase (PPP) gene family (PPP1C, PPP2C, PPP3C/calcineurin, PPP4C, PPP5C, PPP6C, and (PPP) gene family (PPP1C, PPP2C, PPP3C/calcineurin, PPP4C, PPP5C, PPP6C, and PPPEF/PP7), PPPEF/PP7), a subcategory of the broader class of protein serine/threonine phosphatases, catalyze a subcategory of the broader class of protein serine/threonine phosphatases, catalyze dephosphorylation dephosphorylation at seryl and threonyl p-sites

Summary

Introduction

Protein phosphorylation increases the functional diversity of the proteome and is critical to the regulation of numerous cellular processes. The presence or absence of a phosphoryl group at a p-site impacts protein structure, enzyme activity, interactions with other proteins, transport properties, and, cell function and metabolism [2]. Countering the action of phosphoryl attachment by protein kinase enzymes (phosphorylation), the protein phosphatases catalyze the hydrolysis that liberates a phosphate ion and restores the p-site residue (dephosphorylation). The hydroxyl groups of serine, threonine, and tyrosine are amenable to phosphoryl attachment via Catalysts 2020, 10, 674; doi:10.3390/catal10060674 www.mdpi.com/journal/catalysts. Catalysts 2019, 9, x FOR PEER REVIEW to phosphoryl attachment via a phosphoester bond, and most p-sites are one of these three amino a phosphoester bond, and most p-sites are one of these three amino acids, with serine dominant, acids, with serine dominant, threonine second, and tyrosine a distant third [3]. The PPPs share a highly conserved catalytic core [4]

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