Issue 6, 2014

A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase

Abstract

Combined quantum mechanics/molecular mechanics (QM/MM) simulations of the reaction catalysed by phosphite dehydrogenase (PTDH) identify Met53 as important for catalysis. This catalytic role is verified by experiments (including replacement by norleucine and selenomethionine), which show that mutation of this residue significantly affects kcat, without changing KM for phosphite. QM/MM and ab initio QM calculations show that the catalytic effect is electrostatic in nature. The side chain of Met53 specifically stabilizes the transition state for the hydride transfer step of the reaction catalysed by PTDH, forming a ‘face-on’ interaction with His292. To our knowledge, a defined catalytic role for methionine in an enzyme (as opposed to a steric or binding effect, or interaction with a metal ion) has not previously been identified. Analyses of the Protein Data Bank and Cambridge Structural Database indicate that this type of interaction may be relatively widespread, with implications for enzyme-catalysed reaction mechanisms and protein structure.

Graphical abstract: A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase

Supplementary files

Article information

Article type
Edge Article
Submitted
30 okt 2013
Accepted
17 feb 2014
First published
18 feb 2014
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2014,5, 2191-2199

Author version available

A catalytic role for methionine revealed by a combination of computation and experiments on phosphite dehydrogenase

K. E. Ranaghan, J. E. Hung, G. J. Bartlett, T. J. Mooibroek, J. N. Harvey, D. N. Woolfson, W. A. van der Donk and A. J. Mulholland, Chem. Sci., 2014, 5, 2191 DOI: 10.1039/C3SC53009D

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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