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Is the 5,10-methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism?
Henrique Fernandes, Sérgio Sousa, Nuno Cerqueira
UCIBIO@REQUIMTE, BioSIM, Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal

Published: 17 December 2018 by MDPI AG in Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition in MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition session EJIBCE-02: Meeting of Young Researchers in Structural Computational Biology, Porto, Portugal, 2018
MDPI AG, 10.3390/mol2net-04-06004
Abstract:

The 5,10-methylenetetrahydrofolate (5,10-mTHF) is a cofactor essential for the synthesis of purines and thymidine, which are crucial for the cell viability.[1] The α-elimination of ʟ-serine, catalyzed by the serine hydroxymethyltransferase (SHMT), is the primary source of 5,10-mTHF in the cell. However, the catalytic mechanism behind the synthesis of 5,10-mTHF was unknown, and two divergent theories were proposed for the mechanism. Some authors suggested that the final steps of the 5,10-mTHF synthesis occur in the cytoplasm whereas other authors showed some evidence that the reaction must occur inside the SHMT. [2]

In this study, we addressed the entire catalytic mechanism of the PLP-dependent enzyme SHMT using a QM/MM approach and the mechanism of 5,10-mTHF synthesis in aqueous solution. The calculations were prepared and analyzed using molUP [3] for VMD and run on Gaussian09 and ORCA.

This work [4] resulted in the entire e detailed catalytic mechanism of SHMT. The results showed that both hypotheses for the synthesis of 5,10-mTHF shared the two first steps where the -OH group is transferred from the serine to the THF. These reactions occur inside the SHMT and have a ∆G of 18.0 and 2.0 kcal/mol. Then, the reaction can proceed inside the enzyme through 5 sequential steps or in the cytoplasm where only 3 steps are needed. The calculations showed that the mechanism is kinetic and thermodynamically favorable by 0.8 and 24.3 kcal/mol, respectively, when it takes place inside the SHMT. Although the reaction is not impossible in solution, it is very improbable that the THF intermediate might be released to the cytoplasm to overcome a set of reactions that are less favorable when compared to the ones that would occur in the SHMT.

Reference

[1] Froese, D. S.; et al., Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nature comm 2018, 9 (1), 2261-2261.

[2] Schirch, V.; et al, Serine hydroxymethyltransferase revisited. Curr Opin Chem Biol 2005, 9 (5), 482-7.

[3] Fernandes, H. S.; et al., molUP: A VMD plugin to handle QM and ONIOM calculations using the Gaussian software. J Comput Chem 2018, 39 (19), 1344-1353.

[4] Fernandes, H. S.; et al., Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catalysis 2018, 10096-10110.

Acknowledgments

FCT (SFRH/BD/115396/2016, IF/01310/2013, IF/00052/2014 e PTDC/QUI-QFI/31689/2017)

Keywords: Viability, phosphorylation, Methylenetetrahydrofolate, structural, serine, Shmt, steps, MTHF, Hydroxymethyltransferase
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