Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation

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Publikace nespadá pod Filozofickou fakultu, ale pod Středoevropský technologický institut. Oficiální stránka publikace je na webu muni.cz.
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JANOŠ Pavel TVAROŠKA Igor DELLAGO Christoph KOČA Jaroslav

Rok publikování 2020
Druh Článek v odborném periodiku
Časopis / Zdroj ACS Omega
Fakulta / Pracoviště MU

Středoevropský technologický institut

Citace
www https://doi.org/10.1021/acsomega.0c01434
Doi http://dx.doi.org/10.1021/acsomega.0c01434
Klíčová slova Chemical structure; Hydroxyls; Reaction mechanisms; Transition states; Computational chemistry
Popis We applied the transition path sampling (TPS) method to study the translocation step of the catalytic mechanism of galactofuranosyl transferase 2 (GlfT2). Using TPS in the field of enzymatic reactions is still relatively rare, and we show its effectiveness on this enzymatic system. We decipher an unknown mechanism of the translocation step and, thus, provide a complete understanding of the catalytic mechanism of GlfT2 at the atomistic level. The GlfT2 enzyme is involved in the formation of the mycobacterial cell wall and transfers galactofuranose (Galf) from UDP-Galf onto a growing acceptor Galf chain. The biosynthesis of the galactan chain is accomplished in a processive manner, with the growing acceptor substrate remaining bound to GlfT2. The glycosidic bond formed by GlfT2 between the two Gall residues alternates between beta-(1-6) and beta-(1-5) linkages. The translocation of the growing galactan between individual additions of Galf residues is crucial for the function of GlfT2. Analysis of unbiased trajectory ensembles revealed that the translocation proceeds differently depending on the glycosidic linkage between the last two Galf residues. We also showed that the protonation state of the catalytic residue Asp372 significantly influences the translocation. Approximate transition state structures and potential energy reaction barriers of the translocation process were determined. The calculated potential reaction barriers in the range of 6-14 kcal/mol show that the translocation process is not the rate-limiting step in galactan biosynthesis.
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