4LY6

Nucleotide-induced asymmetry within ATPase activator ring drives s54-RNAP interaction and ATP hydrolysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Nucleotide-induced asymmetry within ATPase activator ring drives sigma 54-RNAP interaction and ATP hydrolysis.

Sysoeva, T.A.Chowdhury, S.Guo, L.Nixon, B.T.

(2013) Genes Dev. 27: 2500-2511

  • DOI: 10.1101/gad.229385.113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconst ...

    It is largely unknown how the typical homomeric ring geometry of ATPases associated with various cellular activities enables them to perform mechanical work. Small-angle solution X-ray scattering, crystallography, and electron microscopy (EM) reconstructions revealed that partial ATP occupancy caused the heptameric closed ring of the bacterial enhancer-binding protein (bEBP) NtrC1 to rearrange into a hexameric split ring of striking asymmetry. The highly conserved and functionally crucial GAFTGA loops responsible for interacting with σ54-RNA polymerase formed a spiral staircase. We propose that splitting of the ensemble directs ATP hydrolysis within the oligomer, and the ring's asymmetry guides interaction between ATPase and the complex of σ54 and promoter DNA. Similarity between the structure of the transcriptional activator NtrC1 and those of distantly related helicases Rho and E1 reveals a general mechanism in homomeric ATPases whereby complex allostery within the ring geometry forms asymmetric functional states that allow these biological motors to exert directional forces on their target macromolecules.


    Related Citations: 
    • Crystallization and preliminary X-ray analysis of a sigma54-dependent transcription activator NtrC1 from Aquifex aeolicus bound to ground state ATP analog
      Sysoeva, T.A.,Yennawar, N.,Allaire, M.,Nixon, B.T.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 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, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X
268Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ntrC1
Find proteins for O67198 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67198
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
L, X
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, G, H, I, J, K, M, N, O, P, Q, S, T, U, V, W
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
08T
Query on 08T

Download SDF File 
Download CCD File 
A, B, C, D, E, G, H, I, J, K, M, N, O, P, Q, S, T, U, V, W
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
C10 H14 Be F3 N5 O10 P2
WOGYHYSOODLXII-KWIZKVQNSA-J
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 119.339α = 90.00
b = 130.037β = 89.73
c = 206.368γ = 89.90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
PHASERphasing
d*TREKdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-04
    Type: Initial release