1NY6

Crystal structure of sigm54 activator (AAA+ ATPase) in the active state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains

Lee, S.Y.de la Torre, A.Yan, D.Kustu, S.Nixon, B.T.Wemmer, D.E.

(2003) Genes Dev 17: 2552-2563

  • DOI: https://doi.org/10.1101/gad.1125603
  • Primary Citation of Related Structures:  
    1NY5, 1NY6

  • PubMed Abstract: 

    Transcription by sigma54 RNA polymerase depends on activators that contain ATPase domains of the AAA+ class. These activators, which are often response regulators of two-component signal transduction systems, remodel the polymerase so that it can form open complexes at promoters. Here, we report the first crystal structures of the ATPase domain of an activator, the NtrC1 protein from the extreme thermophile Aquifex aeolicus. This domain alone, which is active, crystallized as a ring-shaped heptamer. The protein carrying both the ATPase and adjacent receiver domains, which is inactive, crystallized as a dimer. In the inactive dimer, one residue needed for catalysis is far from the active site, and extensive contacts among the domains prevent oligomerization of the ATPase domain. Oligomerization, which completes the active site, depends on surfaces that are buried in the dimer, and hence, on a rearrangement of the receiver domains upon phosphorylation. A motif in the ATPase domain known to be critical for coupling energy to remodeling of polymerase forms a novel loop that projects from the middle of an alpha helix. The extended, structured loops from the subunits of the heptamer localize to a pore in the center of the ring and form a surface that could contact sigma54.


  • Organizational Affiliation

    Graduate Group in Biophysics, University of California, Berkeley, California 94720,USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
transcriptional regulator (NtrC family)
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N
267Aquifex aeolicusMutation(s): 0 
Gene Names: NtrC1
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
AA [auth M]
BA [auth N]
O [auth A]
P [auth B]
Q [auth C]
AA [auth M],
BA [auth N],
O [auth A],
P [auth B],
Q [auth C],
R [auth D],
S [auth E],
T [auth F],
U [auth G],
V [auth H],
W [auth I],
X [auth J],
Y [auth K],
Z [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.329 
  • R-Value Work: 0.266 
  • R-Value Observed: 0.266 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.788α = 70.25
b = 108.265β = 85.9
c = 110.02γ = 73.27
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations