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TitleStructural underpinnings of nitrogen regulation by the prototypical nitrogen-responsive transcriptional factor NrpR.
Journal, issue, pagesStructure, Vol. 18, Issue 11, Page 1512-1521, Year 2010
Publish dateNov 10, 2010
AuthorsGoragot Wisedchaisri / David M Dranow / Thomas J Lie / Jeffrey B Bonanno / Yury Patskovsky / Sinem A Ozyurt / J Michael Sauder / Steven C Almo / Stephen R Wasserman / Stephen K Burley / John A Leigh / Tamir Gonen /
PubMed AbstractPlants 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. ...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.
External linksStructure / PubMed:21070950 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.5 - 25.0 Å
Structure data

EMDB-5221:
Nitrogen-Responsive Transcription Factor NrpR form Methanococcus maripaludis in an apo form
Method: EM (single particle) / Resolution: 25.0 Å

EMDB-5222:
Nitrogen-Responsive Transcription Factor NrpR form Methanococcus maripaludis in a 2OG-bound (inhibited) state
Method: EM (single particle) / Resolution: 22.0 Å

PDB-3nek:
Crystal structure of a nitrogen repressor-like protein MJ0159 from Methanococcus jannaschii
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

Chemicals

ChemComp-GOL:
GLYCEROL / Glycerol

ChemComp-HOH:
WATER / Water

Source
  • Methanococcus maripaludis (archaea)
  • methanocaldococcus jannaschii (archaea)
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC

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