6Q6R

Recognition of different base tetrads by RHAU: X-ray crystal structure of G4 recognition motif bound to the 3-end tetrad of a DNA G-quadruplex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Recognition of different base tetrads by RHAU: X-ray crystal structure of the G4 recognition motif bound to the 3'-end tetrad of a DNA G-quadruplex.

Heddi, B.Vee Cheong, V.Schmitt, E.Mechulam, Y.Tuan Phan, A.

(2019) J.Struct.Biol. --: --

  • DOI: 10.1016/j.jsb.2019.10.001

  • PubMed Abstract: 
  • G-quadruplexes (G4) are secondary structures of nucleic acids that can form in cells and have diverse biological functions. Several biologically important proteins interact with G-quadruplexes, of which RHAU - a helicase from the DEAH-box superfamily ...

    G-quadruplexes (G4) are secondary structures of nucleic acids that can form in cells and have diverse biological functions. Several biologically important proteins interact with G-quadruplexes, of which RHAU - a helicase from the DEAH-box superfamily, was shown to bind and unwind G-quadruplexes efficiently. We report a X-ray co-crystal structure at 1.5 Å resolution of an N-terminal fragment of RHAU bound to the exposed tetrad of a parallel-stranded G-quadruplex. The RHAU peptide folds into an L-shaped α-helix, and binds to the G-quadruplex through π-stacking and electrostatic interactions. X-ray crystal structure of our complex identified key amino acid residues important for G-quadruplex-peptide binding interaction at the 3'-end G•G•G•G tetrad. Together with previous solution and crystal structures of RHAU bound to the 5'-end G•G•G•G and G•G•A•T tetrads, our crystal structure highlights the occurrence of a robust G-quadruplex recognition motif within RHAU that can adapt to different accessible tetrads.


    Organizational Affiliation

    School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore.,Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS UMR 8113, Ecole Normale Supérieure Paris-Saclay, 61 Avenue du président Wilson, Cachan 94235, France; School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore. Electronic address: brahim.heddi@ens-cachan.fr.,Laboratoire de Biochimie, UMR 7654, École Polytechnique, Centre National de la Recherche Scientifique, Palaiseau 91128, France.,Laboratoire de Biologie et de Pharmacologie Appliquée, CNRS UMR 8113, Ecole Normale Supérieure Paris-Saclay, 61 Avenue du président Wilson, Cachan 94235, France; NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore. Electronic address: phantuan@ntu.edu.sg.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP-dependent DNA/RNA helicase DHX36
E, F, G, H
29Homo sapiensMutation(s): 0 
Gene Names: DHX36 (DDX36, KIAA1488, MLEL1, RHAU)
EC: 3.6.4.12, 3.6.4.13
Find proteins for Q9H2U1 (Homo sapiens)
Go to Gene View: DHX36
Go to UniProtKB:  Q9H2U1
Entity ID: 1
MoleculeChainsLengthOrganism
Parallel stranded DNA G-quadruplexA,B,C,D16unidentified
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.390α = 90.00
b = 42.250β = 99.30
c = 61.404γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Singapore)SingaporeNRF-NRFI2017-09
Ministry of Education (Singapore)SingaporeMOE2012-T3-1-001

Revision History 

  • Version 1.0: 2019-10-16
    Type: Initial release