1. Structural Underpinnings of Nitrogen Regulation by the Prototypical Nitrogen-Responsive Transcriptional Factor NrpR
- Author
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Stephen K. Burley, John A. Leigh, S.R. Wasserman, Goragot Wisedchaisri, Steven C. Almo, Yury Patskovsky, Tamir Gonen, Jeffrey B. Bonanno, Thomas J. Lie, Sinem A. Ozyurt, David M. Dranow, and J. Michael Sauder
- Subjects
Models, Molecular ,Nitrogen ,Protein Conformation ,Methanococcus ,PII Nitrogen Regulatory Proteins ,Nitrogen assimilation ,Molecular Dynamics Simulation ,Biology ,Structural genomics ,Biological pathway ,03 medical and health sciences ,chemistry.chemical_compound ,Transcription (biology) ,Structural Biology ,Gene ,Molecular Biology ,030304 developmental biology ,2. Zero hunger ,Regulation of gene expression ,0303 health sciences ,030306 microbiology ,Quaternary Ammonium Compounds ,Microscopy, Electron ,Metabolic pathway ,chemistry ,Biochemistry ,Ketoglutaric Acids ,Gene Expression Regulation, Archaeal ,DNA ,Transcription Factors - Abstract
Summary Plants and microorganisms reduce environmental inorganic nitrogen to ammonium, which then enters various metabolic pathways solely via conversion of 2-oxoglutarate (2OG) to glutamate and glutamine. Cellular 2OG concentrations increase during nitrogen starvation. We recently identified a family of 2OG-sensing proteins—the nitrogen regulatory protein NrpR—that bind DNA and repress transcription of nitrogen assimilation genes. We used X-ray crystallography to determine the structure of NrpR regulatory domain. We identified the NrpR 2OG-binding cleft and show that residues predicted to interact directly with 2OG are conserved among diverse classes of 2OG-binding proteins. We show that high levels of 2OG inhibit NrpRs ability to bind DNA. Electron microscopy analyses document that NrpR adopts different quaternary structures in its inhibited 2OG-bound state compared with its active apo state. Our results indicate that upon 2OG release, NrpR repositions its DNA-binding domains correctly for optimal interaction with DNA thereby enabling gene repression.
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