Unraveling the molecular mechanisms of nitrogenase conformational protection against oxygen in diazotrophic bacteria

Background: G. diazotrophicus and A. vinelandii are aerobic
nitrogen-fixing bacteria. Although oxygen is essential for the
survival of these organisms, it irreversibly inhibits nitrogenase,
the complex responsible for nitrogen fixation. Both microorganisms
deal with this paradox through compensatory mechanisms. In A.
vinelandii a conformational protection mechanism occurs through the
interaction between the nitrogenase complex and the FeSII protein.
Previous studies suggested the existence of a similar system in G.
diazotrophicus, but the putative protein involved was not yet
described. This study intends to identify the protein coding gene
in the recently sequenced genome of G. diazotrophicus and also
provide detailed structural information of nitrogenase
conformational protection in both organisms. Results: Genomic
analysis of G. diazotrophicus sequences revealed a protein coding
ORF (Gdia0615) enclosing a conserved "fer2" domain, typical of the
ferredoxin family and found in A. vinelandii FeSII. Comparative
models of both FeSII and Gdia0615 disclosed a conserved beta-grasp
fold. Cysteine residues that coordinate the 2[Fe-S] cluster are in
conserved positions towards the metallocluster. Analysis of solvent
accessible residues and electrostatic surfaces unveiled an
hydrophobic dimerization interface. Dimers assembled by molecular
docking presented a stable behaviour and a proper accommodation of
regions possibly involved in binding of FeSII to nitrogenase
throughout molecular dynamics simulations in aqueous solution.
Molecular modeling of the nitrogenase complex of G. diazotrophicus
was performed and models were compared to the crystal structure of
A. vinelandii nitrogenase. Docking experiments of FeSII and
Gdia0615 with its corresponding nitrogenase complex pointed out in
both systems a putative binding site presenting shape and charge
complementarities at the Fe-protein/MoFe-protein complex interface.
Conclusions: The identification of the putative FeSII coding gene
in G. diazotrophicus genome represents a large step towards the
understanding of the conformational protection mechanism of
nitrogenase against oxygen. In addition, this is the first study
regarding the structural complementarities of FeSII-nitrogenase
interactions in diazotrophic bacteria. The combination of
bioinformatic tools for genome analysis, comparative protein
modeling, docking calculations and molecular dynamics provided a
powerful strategy for the elucidation of molecular mechanisms and
structural features of FeSII-nitrogenase interaction.