4CJ9

BurrH DNA-binding protein from Burkholderia rhizoxinica in its apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bud, a Helix-Loop-Helix DNA-Binding Domain for Genome Modification

Stella, S.Molina, R.Lopez-Mendez, B.Juillerat, A.Bertonati, C.Daboussi, F.Campos-Olivas, R.Duchateau, P.Montoya, G.

(2014) Acta Crystallogr.,Sect.D 70: 2042

  • DOI: 10.1107/S1399004714011183
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy ...

    DNA editing offers new possibilities in synthetic biology and biomedicine for modulation or modification of cellular functions to organisms. However, inaccuracy in this process may lead to genome damage. To address this important problem, a strategy allowing specific gene modification has been achieved through the addition, removal or exchange of DNA sequences using customized proteins and the endogenous DNA-repair machinery. Therefore, the engineering of specific protein-DNA interactions in protein scaffolds is key to providing `toolkits' for precise genome modification or regulation of gene expression. In a search for putative DNA-binding domains, BurrH, a protein that recognizes a 19 bp DNA target, was identified. Here, its apo and DNA-bound crystal structures are reported, revealing a central region containing 19 repeats of a helix-loop-helix modular domain (BurrH domain; BuD), which identifies the DNA target by a single residue-to-nucleotide code, thus facilitating its redesign for gene targeting. New DNA-binding specificities have been engineered in this template, showing that BuD-derived nucleases (BuDNs) induce high levels of gene targeting in a locus of the human haemoglobin β (HBB) gene close to mutations responsible for sickle-cell anaemia. Hence, the unique combination of high efficiency and specificity of the BuD arrays can push forward diverse genome-modification approaches for cell or organism redesign, opening new avenues for gene editing.


    Organizational Affiliation

    Macromolecular Crystallography Group, Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain.,Spectroscopy and NMR Unit, Spanish National Cancer Research Centre (CNIO), Calle de Melchor Fernández Almagro 3, 28029 Madrid, Spain.,Cellectis, 8 Rue de la Croix Jarry, 75013 Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BURRH
A, B
794Paraburkholderia rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454)Mutation(s): 0 
Gene Names: bat1
Find proteins for E5AV36 (Paraburkholderia rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454))
Go to UniProtKB:  E5AV36
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SE
Query on SE

Download SDF File 
Download CCD File 
A
SELENIUM ATOM
Se
SPVXKVOXSXTJOY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.214 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.180 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 73.314α = 90.00
b = 73.314β = 90.00
c = 268.337γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references