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PDBsum entry 3la2

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protein ligands Protein-protein interface(s) links
Transcription PDB id
3la2
Jmol
Contents
Protein chains
196 a.a. *
Ligands
AKG ×2
Waters ×120
* Residue conservation analysis
PDB id:
3la2
Name: Transcription
Title: Crystal structure of ntca in complex with 2-oxoglutarate
Structure: Global nitrogen regulator. Chain: a, b. Synonym: DNA-binding protein vf1, nitrogen-responsive regul protein. Engineered: yes
Source: Anabaena. Organism_taxid: 103690. Strain: pcc 7120. Gene: alr4392, bifa, ntca. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.60Å     R-factor:   0.224     R-free:   0.268
Authors: M.X.Zhao,Y.L.Jiang,Y.X.He,Y.F.Chen,Y.B.Teng,Y.X.Chen,C.C.Zha C.Z.Zhou
Key ref: M.X.Zhao et al. (2010). Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate. Proc Natl Acad Sci U S A, 107, 12487-12492. PubMed id: 20616047
Date:
06-Jan-10     Release date:   14-Jul-10    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A4U6  (NTCA_NOSS1) -  Global nitrogen regulator
Seq:
Struc:
223 a.a.
196 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   1 term 
  Biological process     transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     2 terms  

 

 
Proc Natl Acad Sci U S A 107:12487-12492 (2010)
PubMed id: 20616047  
 
 
Structural basis for the allosteric control of the global transcription factor NtcA by the nitrogen starvation signal 2-oxoglutarate.
M.X.Zhao, Y.L.Jiang, Y.X.He, Y.F.Chen, Y.B.Teng, Y.Chen, C.C.Zhang, C.Z.Zhou.
 
  ABSTRACT  
 
2-oxogluatarate (2-OG), a metabolite of the highly conserved Krebs cycle, not only plays a critical role in metabolism, but also constitutes a signaling molecule in a variety of organisms ranging from bacteria to plants and animals. In cyanobacteria, the accumulation of 2-OG constitutes the signal of nitrogen starvation and NtcA, a global transcription factor, has been proposed as a putative receptor for 2-OG. Here we present three crystal structures of NtcA from the cyanobacterium Anabaena: the apoform, and two ligand-bound forms in complex with either 2-OG or its analogue 2,2-difluoropentanedioic acid. All structures assemble as homodimers, with each subunit composed of an N-terminal effector-binding domain and a C-terminal DNA-binding domain connected by a long helix (C-helix). The 2-OG binds to the effector-binding domain at a pocket similar to that used by cAMP in catabolite activator protein, but with a different pattern. Comparative structural analysis reveals a putative signal transmission route upon 2-OG binding. A tighter coiled-coil conformation of the two C-helices induced by 2-OG is crucial to maintain the proper distance between the two F-helices for DNA recognition. Whereas catabolite activator protein adopts a transition from off-to-on state upon cAMP binding, our structural analysis explains well why NtcA can bind to DNA even in its apoform, and how 2-OG just enhances the DNA-binding activity of NtcA. These findings provided the structural insights into the function of a global transcription factor regulated by 2-OG, a metabolite standing at a crossroad between carbon and nitrogen metabolisms.