8JRC | pdb_00008jrc

Crystal structure of the GAF domain of the transcriptional activator NifA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Formation of NifA-P II complex represses ammonium-sensitive nitrogen fixation in diazotrophic proteobacteria lacking NifL.

Zeng, Y.Guo, L.Gao, Y.Cui, L.Wang, M.Huang, L.Jiang, M.Liu, Y.Zhu, Y.Xiang, H.Li, D.F.Zheng, Y.

(2024) Cell Rep 43: 114476-114476

  • DOI: https://doi.org/10.1016/j.celrep.2024.114476
  • Primary Citation of Related Structures:  
    8JRC

  • PubMed Abstract: 

    Biological nitrogen fixation catalyzed by nitrogenase contributes greatly to the global nitrogen cycle. Nitrogenase expression is subject to regulation in response to nitrogen availability. However, the mechanism through which the transcriptional activator NifA regulates nitrogenase expression by interacting with P II nitrogen regulatory proteins remains unclear in diazotrophic proteobacteria lacking NifL. Here, we demonstrate that in Rhodopseudomonas palustris grown with ammonium, NifA bound deuridylylated P II proteins to form an inactive NifA-P II complex, thereby inhibiting the expression of nitrogenase. Upon nitrogen limitation, the dissociation of uridylylated P II proteins from NifA resulted in the full restoration of NifA activity, and, simultaneously, uridylylation of the significantly up-regulated P II protein GlnK2 led to the increased expression of NifA in R. palustris. This insight into how NifA interacts with P II proteins and controls nitrogenase expression sets the stage for creating highly efficient diazotrophs, reducing the need for energy-intensive chemical fertilizers and helping to diminish carbon emissions.


  • Organizational Affiliation
    • State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nif-specific regulatory protein
A, B
209Rhodopseudomonas palustrisMutation(s): 0 
Gene Names: nifA
UniProt
Find proteins for A0A2P0ZWG8 (Rhodopseudomonas palustris)
Explore A0A2P0ZWG8 
Go to UniProtKB:  A0A2P0ZWG8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2P0ZWG8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.631α = 90
b = 70.093β = 113.06
c = 55.039γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91851102

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-19
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references, Structure summary