3O5T

Structure of DraG-GlnZ complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction

Rajendran, C.Gerhardt, E.C.M.Bjelic, S.Gasperina, A.Scarduelli, M.Pedrosa, F.O.Chubatsu, L.S.Merrick, M.Souza, E.M.Winkler, F.K.Huergo, L.F.Li, X.-D.

(2011) Proc Natl Acad Sci U S A 108: 18972-18976

  • DOI: https://doi.org/10.1073/pnas.1108038108
  • Primary Citation of Related Structures:  
    3O5T

  • PubMed Abstract: 

    Nitrogen metabolism in bacteria and archaea is regulated by a ubiquitous class of proteins belonging to the P(II)family. P(II) proteins act as sensors of cellular nitrogen, carbon, and energy levels, and they control the activities of a wide range of target proteins by protein-protein interaction. The sensing mechanism relies on conformational changes induced by the binding of small molecules to P(II) and also by P(II) posttranslational modifications. In the diazotrophic bacterium Azospirillum brasilense, high levels of extracellular ammonium inactivate the nitrogenase regulatory enzyme DraG by relocalizing it from the cytoplasm to the cell membrane. Membrane localization of DraG occurs through the formation of a ternary complex in which the P(II) protein GlnZ interacts simultaneously with DraG and the ammonia channel AmtB. Here we describe the crystal structure of the GlnZ-DraG complex at 2.1 Å resolution, and confirm the physiological relevance of the structural data by site-directed mutagenesis. In contrast to other known P(II) complexes, the majority of contacts with the target protein do not involve the T-loop region of P(II). Hence this structure identifies a different mode of P(II) interaction with a target protein and demonstrates the potential for P(II) proteins to interact simultaneously with two different targets. A structural model of the AmtB-GlnZ-DraG ternary complex is presented. The results explain how the intracellular levels of ATP, ADP, and 2-oxoglutarate regulate the interaction between these three proteins and how DraG discriminates GlnZ from its close paralogue GlnB.


  • Organizational Affiliation

    Macromolecular Crystallography, Swiss Light Source, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dinitrogenase reductase activacting glicohydrolase297Azospirillum brasilenseMutation(s): 0 
Gene Names: draG
EC: 3.2.2.24
UniProt
Find proteins for A7XNI2 (Azospirillum brasilense)
Explore A7XNI2 
Go to UniProtKB:  A7XNI2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA7XNI2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PII-like protein Pz112Azospirillum brasilenseMutation(s): 0 
Gene Names: glnZ
UniProt
Find proteins for P70731 (Azospirillum brasilense)
Explore P70731 
Go to UniProtKB:  P70731
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP70731
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.153 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.654α = 90
b = 115.654β = 90
c = 105.626γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2013-03-13
    Changes: Database references
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description