Molecular-Genetic and Structural Analyses of the NifHDKX Proteins of the Nitrogenase System
The nitrogenase enzyme is the biochemical machiner responsible for the conversion of the largely unavailable nitrogen to the easily assimilable ammonia for living organisms by the process termed as biological nitrogen fixation (BNF). This study was focused on understanding the various structural and functional aspects of the nitrogenase enzyme related to maturation and assembly of the FeMo-cofactor (FeMoco) metallocluster of the MoFe protein (the site for final substrate reduction), development of a dimeric MoFe protein and the structural homology of nitrogenase with other metalloenzymes. This research was specifically directed towards the NifHDKX proteins in which the nifHDK genes are the major structural genes that encode the nitrogenase enzyme and nifX is an accessory gene that encodes the NifX protein, indicated to be involved in the formation of the FeMoco. The overall objective of this study was to gain structural and functional information on the nitrogenase enzyme through the study of the NifHDKX proteins. A major part of our study included the detection of protein-protein interactions between the NifD, NifK and a fused NifDK protein. The results of this study could prove to be useful for further studies that are directed towards condensing the nif genes so as to facilitate transfer of nitrogen fixing genes to plants for their improved nutrition. We also determined protein-protein interactions between NifX and other proteins involved in the FeMoco biosynthetic pathway. Based on the results, we were able to describe the role of NifX and propose a modified model for the FeMoco biosynthesis pathway. Apart from this, a comparative structural and evolutionary study was performed on the NifH similar proteins such as ChlL, CompA, MinD and ArsA and the NifDK similar proteins known as ChlBN. Based on the conservation of similar structural domains in NifH and ArsA, NifH was found to complement the function of ArsA1. Also the comparison between NifDK and the homology modeled ChlBN protein structure suggested a potential site for the presence of a FeMoco in ChlN. Thus, these studies helped us to derive meaningful conclusions on the structure and evolution of the nitrogenase enzyme and its homologs in nature.