Author ORCID Identifier

https://orcid.org/0000-0002-2956-9781

Document Type

Article

Publication Date

2012

Publication Title

The Journal of Physical Chemistry

Volume

116

Issue

48

First Page

14040

Last Page

14050

DOI

10.1021/jp310952c

Abstract

UDP-galactopyranose mutase (UGM) is a key flavoenzyme involved in cell wall biosynthesis of a variety of pathogenic bacteria and hence, integral to their survival. It catalyzes the interconversion of UDP-galactopyranose (UDP-Galp) and UDP-galactofuranose (UDP-Galf); interconversion of the galactose moieties six- and five-membered ring forms. We have synergistically applied both density functional theory (DFT)-cluster and ONIOM quantum mechanics/molecular mechanics (QM/MM) hybrid calculations to elucidate the mechanism of this important enzyme and to provide insight into its uncommon mechanism. It is shown that the flavin must initially be in its fully reduced form. Furthermore, it requires an N5FAD–H proton, which, through a series of tautomerizations, is transferred onto the ring oxygen of the substrate’s Galp moiety to facilitate ring-opening with concomitant Schiff base formation. Conversely, Galf formation is achieved via a series of tautomerizations involving proton transfer from the galactose’s −O4GalH group ultimately onto the flavin’s N5FAD center. With the DFT-cluster model, the overall rate-limiting step with a barrier of 120.0 kJ mol–1 is the interconversion of two Galf-flavin tautomers: one containing a C4FAD–OH group and the other a tetrahedral protonated-N5FAD center. In contrast, in the QM/MM model a considerably more extensive chemical model was used that included all of the residues surrounding the active site, and modeled both their steric and electrostatic effects. In this approach, the overall rate-limiting step with a barrier of 99.2 kJ mol–1 occurs during conformational rearrangement of the Schiff base linear galactose–flavin complex. This appears due to the lack of suitable functional groups to facilitate the rearrangement.

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