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Open Access Highly Accessed Research article

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

Mikael Elias1, Dorothee Liebschner2, Jurgen Koepke3, Claude Lecomte2, Benoit Guillot2, Christian Jelsch2 and Eric Chabriere4*

Author Affiliations

1 Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel

2 Cristallographie Résonance Magnétique et Modélisations, CNRS UMR 7036 Université de Lorraine, Vandoeuvre-lès-Nancy, France

3 Max-Planck-Inst. of Biophysics, Department of Molecular Membrane Biol., Frankfurt/Main, Germany

4 Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, IRD/CNRS, Université de la Méditerranée (Aix-Marseille II), 13 385 Marseille, France

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BMC Research Notes 2013, 6:308  doi:10.1186/1756-0500-6-308

Published: 2 August 2013

Abstract

Background

Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms.

Results

A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed.

Conclusions

A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.

Keywords:
Sub-Ångstrom X-ray crystallography; Hydrogen atoms; DFPase; MoPro software