4LY6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: https://doi.org/10.1101/gad.229385.113

  • 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) 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.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, 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, O, P, Q, R, S, T, U, V, W, X
268Aquifex aeolicusMutation(s): 0 
Gene Names: aq_1117ntrC1
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
08T
Query on 08T

Download Ideal Coordinates CCD File 
AA [auth B]
BB [auth Q]
CA [auth C]
DB [auth S]
EA [auth D]
AA [auth B],
BB [auth Q],
CA [auth C],
DB [auth S],
EA [auth D],
FB [auth T],
GA [auth E],
HB [auth U],
IA [auth G],
JB [auth V],
KA [auth H],
LB [auth W],
MA [auth I],
OA [auth J],
QA [auth K],
TA [auth M],
VA [auth N],
XA [auth O],
Y [auth A],
ZA [auth P]
[[[(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
ADP
Query on ADP

Download Ideal Coordinates CCD File 
NB [auth X],
SA [auth L]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth P]
BA [auth B]
CB [auth Q]
DA [auth C]
EB [auth S]
AB [auth P],
BA [auth B],
CB [auth Q],
DA [auth C],
EB [auth S],
FA [auth D],
GB [auth T],
HA [auth E],
IB [auth U],
JA [auth G],
KB [auth V],
LA [auth H],
MB [auth W],
NA [auth I],
PA [auth J],
RA [auth K],
UA [auth M],
WA [auth N],
YA [auth O],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.339α = 90
b = 130.037β = 89.73
c = 206.368γ = 89.9
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Refinement description