3MHY

A New PII Protein Structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A new P(II) protein structure identifies the 2-oxoglutarate binding site.

Truan, D.Huergo, L.F.Chubatsu, L.S.Merrick, M.Li, X.D.Winkler, F.K.

(2010) J.Mol.Biol. 400: 531-539

  • DOI: 10.1016/j.jmb.2010.05.036

  • PubMed 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 ...

    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.


    Organizational Affiliation

    Macromolecular Crystallography, Swiss Light Source, Villigen PSI, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PII-like protein Pz
A, B, C
112Azospirillum brasilenseMutation(s): 0 
Gene Names: glnZ
Find proteins for P70731 (Azospirillum brasilense)
Go to UniProtKB:  P70731
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
AKG
Query on AKG

Download SDF File 
Download CCD File 
A, B, C
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PG6
Query on PG6

Download SDF File 
Download CCD File 
A, B
1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE
C12 H26 O6
DMDPGPKXQDIQQG-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 64.980α = 90.00
b = 87.950β = 90.00
c = 116.880γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
Heididata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-02-13
    Type: Database references, Source and taxonomy