3M0E

Crystal structure of the ATP-bound state of Walker B mutant of NtrC1 ATPase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Engagement of Arginine Finger to ATP Triggers Large Conformational Changes in NtrC1 AAA+ ATPase for Remodeling Bacterial RNA Polymerase.

Chen, B.Sysoeva, T.A.Chowdhury, S.Guo, L.De Carlo, S.Hanson, J.A.Yang, H.Nixon, B.T.

(2010) Structure 18: 1420-1430

  • DOI: 10.1016/j.str.2010.08.018

  • PubMed Abstract: 
  • The NtrC-like AAA+ ATPases control virulence and other important bacterial activities through delivering mechanical work to σ54-RNA polymerase to activate transcription from σ54-dependent genes. We report the first crystal structure for such an ATPas ...

    The NtrC-like AAA+ ATPases control virulence and other important bacterial activities through delivering mechanical work to σ54-RNA polymerase to activate transcription from σ54-dependent genes. We report the first crystal structure for such an ATPase, NtrC1 of Aquifex aeolicus, in which the catalytic arginine engages the γ-phosphate of ATP. Comparing the new structure with those previously known for apo and ADP-bound states supports a rigid-body displacement model that is consistent with large-scale conformational changes observed by low-resolution methods. First, the arginine finger induces rigid-body roll, extending surface loops above the plane of the ATPase ring to bind σ54. Second, ATP hydrolysis permits Pi release and retraction of the arginine with a reversed roll, remodeling σ54-RNAP. This model provides a fresh perspective on how ATPase subunits interact within the ring-ensemble to promote transcription, directing attention to structural changes on the arginine-finger side of an ATP-bound interface.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator (NtrC family)
A, B, C, D, E, F, G
266Aquifex aeolicus (strain VF5)Mutation(s): 1 
Gene Names: ntrC1
Find proteins for O67198 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67198
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.63 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 251.209α = 90.00
b = 242.586β = 90.00
c = 40.703γ = 90.00
Software Package:
Software NamePurpose
ELVESrefinement
PHENIXrefinement
MrBUMPphasing
CrystalCleardata reduction
CrystalCleardata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-11-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description