Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Krachtus, Dieter; Smith, Jeremy; Imhof, Petra

doi:10.3390/molecules23123342

Quantum Mechanical/Molecular Mechanical Analysis of the Catalytic Mechanism of Phosphoserine Phosphatase

Journal Article · Mon Dec 17 00:00:00 EST 2018 · Molecules

DOI:https://doi.org/10.3390/molecules23123342· OSTI ID:1523734

Krachtus, Dieter ^[1]; ^[2]; ^[3]

Interdisciplinary Center for Scientific Computing (IWR), Heidelberg (Germany)
Interdisciplinary Center for Scientific Computing (IWR), Heidelberg (Germany); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Freie Universität Berlin, Berlin (Germany)

Phosphoserine phosphatase (PSP), a member of the haloacid dehalogenase (HAD) superfamily that comprises the vast majority of phosphotransferases, is likely a steady-state regulator of the level of d-serine in the brain. The introduced catalytic cycle of PSP consists of a two-step mechanism: formation of a phospho-enzyme intermediate by phosphate transfer to Asp11 and its subsequent hydrolysis. Our combined quantum mechanical/molecular mechanical (QM/MM) calculations of the reaction pathways favour a dissociative mechanism of nucleophilic substitution via a trigonal-planar metaphosphate-like configuration for both steps, associated with proton transfer to the leaving group or from the nucleophile. This proton transfer is facilitated by active site residue Asp13 that acts as both a general base and a general acid. Free energy calculation on the reaction pathways further support the structural role of the enzymatic environment and the active site architecture. The choice of a proper reaction coordinate along which to bias the free energy calculations can be guided by a projection of the canonical reaction coordinate obtained from a chain-of-state optimisation onto important internal coordinates.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: Deutsche Forschungsgemeinschaft (DFG); USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1523734

Journal Information:: Molecules, Journal Name: Molecules Journal Issue: 12 Vol. 23; ISSN MOLEFW; ISSN 1420-3049

Publisher:: MDPICopyright Statement

Country of Publication:: United States

Language:: English

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