Author ORCID Identifier

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

Document Type

Article

Publication Date

2-2008

Publication Title

The Journal of Physical Chemistry

Volume

112

Issue

11

First Page

3462

Last Page

3569

DOI

10.1021/jp075415m

Abstract

LpxC is a key enzyme in the biochemical synthesis of Lipid A, an important outer cell-membrane component found in a number of pathogenic bacteria. Using DFT, we have investigated the binding of the substrate within its active site as well as the deacetylation mechanism it catalyzes. The substrate is found to preferentially coordinate to the active site Zn2+ via its carbonyl oxygen between a Zn2+-bound H2O and an adjacent threonine (Thr191). Furthermore, upon substrate binding a nearby Glu78 residue is found to readily deprotonate the remaining Zn2+-bound H2O. Unlike several related metallopeptidases, the mechanism of LpxC is found to proceed via four steps; (i) initial hydroxylation of the substrates' carbonyl carbon to give a gem−diolate intermediate, (ii) protonation of the amide nitrogen by the histidine His265−H+, (iii) a barrier-less change in the active site-intermediate hydrogen-bond network and finally, (iv) C−N bond cleavage. Notably, the rate-determining step of the mechanism of LpxC is found to be the initial hydroxylation while the final C−N bond cleavage occurs with an overall barrier of 23.6 kJ mol-1. Furthermore, LpxC uses a general acid/base pair mechanism as indicated by the fact that both His265−H+ and Glu78 are accordingly involved.

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