title: A new P(II) protein structure identifies the 2-oxoglutarate binding site.
abstract: P(II) proteins of bacteria, archaea, and plants regulate many facets of nitrogen metabolism. They do so by interacting with their target proteins, which can be enzymes, transcription factors, or membrane proteins. A key feature of the ability of P(II) proteins to sense cellular nitrogen status and to interact accordingly with their targets is their binding of the key metabolic intermediate 2-oxoglutarate (2-OG). However, the binding site of this ligand within P(II) proteins has been controversial. We have now solved the X-ray structure, at 1.4 A resolution, of the Azospirillum brasilense P(II) protein GlnZ complexed with MgATP and 2-OG. This structure is in excellent agreement with previous biochemical data on 2-OG binding to a variety of P(II) proteins and shows that 2-oxoglutarate binds within the cleft formed between neighboring subunits of the homotrimer. The 2-oxo acid moiety of bound 2-OG ligates the bound Mg(2+) together with three phosphate oxygens of ATP and the side chain of the T-loop residue Gln39. Our structure is in stark contrast to an earlier structure of the Methanococcus jannaschii GlnK1 protein in which the authors reported 2-OG binding to the T-loop of that P(II) protein. In the light of our new structure, three families of T-loop conformations, each associated with a distinct effector binding mode and characterized by a different interaction partner of the ammonium group of the conserved residue Lys58, emerge as a common structural basis for effector signal output by P(II) proteins.
authors.affiliation: Macromolecular Crystallography, Swiss Light Source, Villigen PSI, Switzerland.
authors.forename: Daphne
authors.initials: D
authors.lastname: Truan
authors.forename: Luciano F
authors.initials: LF
authors.lastname: Huergo
authors.forename: Leda S
authors.initials: LS
authors.lastname: Chubatsu
authors.forename: Mike
authors.initials: M
authors.lastname: Merrick
authors.forename: Xiao-Dan
authors.initials: XD
authors.lastname: Li
authors.forename: Fritz K
authors.initials: FK
authors.lastname: Winkler
mesh_terms: D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism; D000595:Amino Acid Sequence; D015806:Azospirillum brasilense / Q000737:chemistry* / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D002413:Cations, Divalent / Q000737:chemistry / Q000378:metabolism; D018360:Crystallography, X-Ray; D007656:Ketoglutaric Acids / Q000378:metabolism*; D008274:Magnesium / Q000737:chemistry / Q000378:metabolism; D017017:Methanococcus / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D051922:PII Nitrogen Regulatory Proteins / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D021122:Protein Subunits / Q000737:chemistry / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D002413:Cations, Divalent; C100965:GlnZ protein, Azospirillum brasilense; D007656:Ketoglutaric Acids; D051922:PII Nitrogen Regulatory Proteins; D021122:Protein Subunits; D000255:Adenosine Triphosphate; D008274:Magnesium