2YPF

Structure of the AvrBs3-DNA complex provides new insights into the initial thymine-recognition mechanism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of the Avrbs3-DNA Complex Provides New Insights Into the Initial Thymine-Recognition Mechanism

Stella, S.Molina, R.Yefimenko, I.Prieto, J.Silva, G.H.Bertonati, C.Juillerat, A.Duchateau, P.Montoya, G.

(2013) Acta Crystallogr.,Sect.D 69: 1707

  • DOI: 10.1107/S0907444913016429

  • PubMed Abstract: 
  • Transcription activator-like effectors contain a DNA-binding domain organized in tandem repeats. The repeats include two adjacent residues known as the repeat variable di-residue, which recognize a single base pair, establishing a direct code between ...

    Transcription activator-like effectors contain a DNA-binding domain organized in tandem repeats. The repeats include two adjacent residues known as the repeat variable di-residue, which recognize a single base pair, establishing a direct code between the dipeptides and the target DNA. This feature suggests this scaffold as an excellent candidate to generate new protein-DNA specificities for biotechnological applications. Here, the crystal structure of AvrBs3 (residues 152-895, molecular mass 82 kDa) in complex with its target DNA sequence is presented, revealing a new mode of interaction with the initial thymine of the target sequence, together with an analysis of both the binding specificity and the thermodynamic properties of AvrBs3. This study quantifies the affinity and the specificity between AvrBs3 and its target DNA. Moreover, in vitro and in vivo analyses reveal that AvrBs3 does not show a strict nucleotide-binding preference for the nucleotide at the zero position of the DNA, widening the number of possible sequences that could be targeted by this scaffold.


    Organizational Affiliation

    Structural Biology and Biocomputing Programme, Spanish Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 28029 Madrid, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AVRBS3
A
758Xanthomonas campestris pv. armoraciaeMutation(s): 0 
Gene Names: hax2
Find proteins for Q3ZD73 (Xanthomonas campestris pv. armoraciae)
Go to UniProtKB:  Q3ZD73
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*TP*TP*AP*TP*AP*TP*AP*AP*AP*CP*CP*TP*AP *AP*CP*CP*CP*TP*CP*TP*AP)-3'B22synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'C21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.236 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 151.110α = 90.00
b = 100.250β = 102.55
c = 61.370γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-09-11
    Type: Database references, Source and taxonomy, Structure summary