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

BMC Research Notes

Eric Chabriere¹  Christian Jelsch²  Benoit Guillot²  Claude Lecomte²  Jurgen Koepke³  Dorothee Liebschner²  Mikael Elias⁴ 

[1] Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, IRD/CNRS, Université de la Méditerranée (Aix-Marseille II), 13 385 Marseille, France;Cristallographie Résonance Magnétique et Modélisations, CNRS UMR 7036 Université de Lorraine, Vandoeuvre-lès-Nancy, France;Max-Planck-Inst. of Biophysics, Department of Molecular Membrane Biol., Frankfurt/Main, Germany;Weizmann Institute of Science, Biological Chemistry, Rehovot, Israel

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

Others  :  1141952
DOI  :  10.1186/1756-0500-6-308

 received in 2013-03-27, accepted in 2013-07-27,  发布年份 2013

【 摘 要 】

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.

【 授权许可】

   
2013 Elias et al.; licensee BioMed Central Ltd.

【 图 表 】

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