The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations

Abstract

In order to elucidate the catalytic mechanism of the Mn-Mn containing serine/threonine protein phosphatase 5 (PP5), we present a density functional theory study with a cluster model approach. According to our results, the reaction occurs through an in-line concerted transition state with an energy of 15.8 kcal mol(-1) , and no intermediates are formed. The important role played by His304 and Asp274 as stabilizers of the leaving group has been shown, whereas the role played by the metal ions seems to be mostly electrostatic. The indispensable requirement of having a neutral active center has been demonstrated by testing different protonation states of the cluster model. We have shown also the importance of describing properly the electronic configuration of the Mn-Mn binuclear centers.

Vanadium and proteins: Uptake, transport, structure, activity and function

“…This approach was used to characterize the active site, the catalytic cycle and the structure of other metal proteins [157] and consists in the simulation of the 51 V hyperfine coupling tensor A of a V IV O complex which can be considered a model for the active site. When 51 V A is calculated using the functional BHandHLYP and the basis set 6-311g(d,p), a good model of the V sites should give A z values in agreement with the experimental one with a deviation around 2-3% [158,159,160,161,162,163,164].…”

Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations

“…[11] It is often observed in the catalytic mechanism of integrases, phosphatases, and α- d -phosphohexomutases. [11a,b, 12] Because all members of the latter superfamily appear to have similar mechanisms of action, a concerted pathway is expected for the human-α-PGM-catalyzed reaction. [11a, 13] However, phosphoryl transfer reaction mechanisms can also proceed through two other different pathways: 1) a stepwise associative mechanism (addition–elimination) in which the nucleophilic attack precedes the departure of the leaving group, and the reaction proceeds through a pentavalent phosphorane intermediate, and 2) a stepwise dissociative mechanism (elimination–addition) in which the leaving group departs prior to the nucleophilic attack with the formation of a metaphosphate intermediate.…”

Computational Biochemistry

“…The reaction's energy profile was obtained from high-level theoretical calculations and was then performed for several DFs already implemented in commonly used software. 86 Aside from being used to validate DFs' performance in particular interactions, pure DFT studies have already proved their value in the biochemistry field. 86 Aside from being used to validate DFs' performance in particular interactions, pure DFT studies have already proved their value in the biochemistry field.…”

“…At the time, this benchmarking has contributed to proceed further toward unveiling the 3 0 -end processing mechanism of HIV-1 protease in DNA, 85 the universal two-metal-ion catalysis in RNA polymerase II, 45b or the in-line concerted catalysis of phosphoserine or phosphothreonine by protein phosphatase 5. 86,87 The PSII is one of the most relevant examples in the past few years. In particular, a combination of DFT calculations and a cluster model approach has shown good results toward the approach of systems with transition metals, such as cobalt and manganese.…”

“…In the recent past, our group has successfully applied QM/MM with the subtractive ONIOM method, on a large number of enzymatic studies including glycoside hydrolases, 86,106 proteases, 107 oxidoreductases, 108 and transferases. 45b,109 We highlight two specific challenging systems, in which the application of this approach proved to be crucial.…”