Revealing the unknown aspects of initial steps of prenylated flavin mononucleotide biosynthesis – the role of Lys129 in PaUbiX

19 May 2022, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Background Prenylated flavin mononucleotide (prFMN) is a recently discovered, heavily modified flavin compound. It is the only known cofactor that enables enzymatic 1,3-dipolar cycloaddition reactions. It is produced by enzymes from the UbiX family, from flavin mononucleotide and either dimethylallyl mono- or diphosphate. prFMN biosynthe-sis is currently reported to be initiated by protonation of the substrate by Glu140. Methods Computational chemistry methods are applied herein - mostly different flavors of molecular dynamics MD, such as Constant pH MD, hybrid Quantum-Mechanical / Molecular Mechanical MD, and classical MD. Results Glu140 competes for a single proton with Lys129 prior to the prFMN biosynthesis but it is the latter that adopted a protonated state throughout most of the simulation time. Lys129 interacts very strongly with Glu140 and it plays a key role in the positioning of the DMAP’s phosphate group within the PaUbiX active site throughout different steps of prFMN biosynthesis Conclusions The role of Lys129 in the functioning of PaUbiX is reported for the first time. The severity of interactions between Glu140, Lys129, and DMAP’s phosphate group might enable an unusual decoupling of phosphate’s protonation from the DMAP’s breakdown. This behavior is most likely conserved throughout the UbiX family to the structur-al resemblance of active sites of those proteins. Significance Mechanistic insights into a crucial biochemical process, biosynthesis of prFMN, are provided. This study, alt-hough purely computational, extends and perfectly complements the knowledge obtained in classical laboratory experiments.

Keywords

UbiX
prenylated flavin mononucleotide
protonation states
phosphate

Supplementary materials

Title
Description
Actions
Title
Supplementary Material
Description
Detailed results of CpH MD simulations along with solvent exposure data, results of predicting protonation states of DMAP and the phosphate, structures of QM cluster optimi-zations, the initial structure of enzyme-adduct system used for CpH MD, QM and QM/MM simulations along with the detailed information regarding how this model was obtained.
Actions

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.