3NBF

Q28E mutant of hera helicase N-terminal domain bound to 8-oxo-ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.

Strohmeier, J.Hertel, I.Diederichsen, U.Rudolph, M.G.Klostermeier, D.

(2011) Biol.Chem. 392: 357-369

  • DOI: 10.1515/BC.2011.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DEAD-box proteins disrupt or remodel RNA and protein/RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and ...

    DEAD-box proteins disrupt or remodel RNA and protein/RNA complexes at the expense of ATP. The catalytic core is composed of two flexibly connected RecA-like domains. The N-terminal domain contains most of the motifs involved in nucleotide binding and serves as a minimalistic model for helicase/nucleotide interactions. A single conserved glutamine in the so-called Q-motif has been suggested as a conformational sensor for the nucleotide state. To reprogram the Thermus thermophilus RNA helicase Hera for use of oxo-ATP instead of ATP and to investigate the sensor function of the Q-motif, we analyzed helicase activity of Hera Q28E. Crystal structures of the Hera N-terminal domain Q28E mutant (TthDEAD_Q28E) in apo- and ligand-bound forms show that Q28E does change specificity from adenine to 8-oxoadenine. However, significant structural changes accompany the Q28E mutation, which prevent the P-loop from adopting its catalytically active conformation and explain the lack of helicase activity of Hera_Q28E with either ATP or 8-oxo-ATP as energy sources. 8-Oxo-adenosine, 8-oxo-AMP, and 8-oxo-ADP weakly bind to TthDEAD_Q28E but in non-canonical modes. These results indicate that the Q-motif not only senses the nucleotide state of the helicase but could also stabilize a catalytically competent conformation of the P-loop and other helicase signature motifs.


    Organizational Affiliation

    Institute for Organic and Biomolecular Chemistry, University of Göttingen, Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heat resistant RNA dependent ATPase
A, B, C, D
207Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 1 
Find proteins for Q72GF3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GF3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
8OD
Query on 8OD

Download SDF File 
Download CCD File 
A, B, C, D
[(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate
C10 H15 N5 O11 P2
RKHXUJRVBUXHAN-UUOKFMHZSA-N
 Ligand Interaction
8OP
Query on 8OP

Download SDF File 
Download CCD File 
C, D
[(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate
C10 H14 N5 O8 P
JPZDUYBDBSYCDZ-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.184 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 60.648α = 68.90
b = 60.676β = 77.29
c = 74.085γ = 72.64
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-08
    Type: Refinement description