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

Mikael Elias, Dorothee Liebschner, Jurgen Koepke, Claude Lecomte, Benoit Guillot, Christian Jelsch, Eric Chabriere

Research output: Contribution to journalArticlepeer-review

20 Scopus citations

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.

Original languageEnglish (US)
Article number308
JournalBMC Research Notes
Volume6
Issue number1
DOIs
StatePublished - 2013

Keywords

  • DFPase
  • Hydrogen atoms
  • MoPro software
  • Sub-Ångstrom X-ray crystallography

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