Crystal structure of the phosphorylated receiver domain of the transcription regulator NtrC1 from Aquifex aeolicus

Experimental Data Snapshot

  • Resolution: 3.03 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 

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Negative regulation of AAA + ATPase assembly by two component receiver domains: a transcription activation mechanism that is conserved in mesophilic and extremely hyperthermophilic bacteria

Doucleff, M.Chen, B.Maris, A.E.Wemmer, D.E.Kondrashkina, E.Nixon, B.T.

(2005) J Mol Biol 353: 242-255

  • DOI: https://doi.org/10.1016/j.jmb.2005.08.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Only a few transcriptional regulatory proteins have been characterized in extremely hyperthermophilic organisms, and most function as repressors. Structural features of the NtrC1 protein from the hyperthermophilic bacterium Aquifex aeolicus suggested that this protein functions similarly to the sigma(54)-polymerase activator DctD of Sinorhizobium meliloti. Here, we demonstrate that NtrC1 is an enzyme that hydrolyzes ATP to activate initiation of transcription by sigma(54)-holoenzyme. New structural data, including small-angle solution scattering data and the crystal structure of the phosphorylated receiver domain, show that NtrC1 uses a signal transduction mechanism very similar to that of DctD to control assembly of its AAA+ ATPase domain. As for DctD, the off-state of NtrC1 depends upon a tight dimer of the receiver domain to repress oligomerization of an intrinsically competent ATPase domain. Activation of NtrC1 stabilizes an alternative dimer configuration of the receiver domain that is very similar to the on-state dimers of the DctD and FixJ receiver domains. This alternative dimer appears to relieve repression of the ATPase domain by disrupting the off-state dimerization interface along the helical linker region between receiver and ATPase domains. Bacterial enhancer binding proteins typically have two linker sequences, one between N-terminal regulatory and central ATPase domains, and one between the central ATPase and C-terminal DNA binding domains. Sequence analyses reveal an intriguing correlation between the negative regulation mechanism of NtrC1 and DctD, and a structured N-terminal linker and unstructured C-terminal one; conversely, the very different, positive mechanism present in NtrC protein occurs in the context of an unstructured N-terminal linker and a structured C-terminal one. In both cases, the structured linkers significantly contribute to the stability of the off-state dimer conformation. These analyses also raise the possibility that a structured linker between N-terminal regulatory and central output domains is used frequently in regulatory proteins from hyperthermophilic organisms.

  • Organizational Affiliation

    Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
transcriptional regulator NtrC1
A, B
150Aquifex aeolicusMutation(s): 1 
Gene Names: NtrC1
Find proteins for O67198 (Aquifex aeolicus (strain VF5))
Explore O67198 
Go to UniProtKB:  O67198
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67198
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on PHD
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 3.03 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.254 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.517α = 90
b = 91.517β = 90
c = 130.942γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description