Structural Underpinnings of Nitrogen Regulation by the Prototypical Nitrogen-Responsive Transcriptional Factor NrpR

• Published in: Structure (London) 2010-11, Vol.18 (11), p.1512-1521
• Main Authors: Wisedchaisri, Goragot, Dranow, David M., Lie, Thomas J., Bonanno, Jeffrey B., Patskovsky, Yury, Ozyurt, Sinem A., Sauder, J. Michael, Almo, Steven C., Wasserman, Stephen R., Burley, Stephen K., Leigh, John A., Gonen, Tamir
• Format: Article
• Language: English
• Subjects: Control; Conversion; Deoxyribonucleic acid; Gene Expression Regulation, Archaeal - genetics; Genes; Ketoglutaric Acids - metabolism; Methanococcus - chemistry; Microscopy, Electron; Models, Molecular; Molecular Dynamics Simulation; Nitrogen - metabolism; Optimization; PII Nitrogen Regulatory Proteins - chemistry; PII Nitrogen Regulatory Proteins - metabolism; Protein Conformation; Proteins; Quaternary Ammonium Compounds - metabolism; Residues; Transcription Factors - chemistry; Transcription Factors - metabolism; X-rays
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2010.08.014

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. ► Structure of the nitrogen regulatory protein in the active and inhibited states ► The identification of conservation of 2OG binding in diverse proteins ► The well-known ferredoxin fold is expanded to reveal a novel fold ► Transcriptional regulation of nitrogen assimilating genes is dynamically controlled