2YPF | pdb_00002ypf

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

• PDB DOI: https://doi.org/10.2210/pdb2YPF/pdb
• NAKB: 2YPF

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xanthomonas campestris, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-30 Released: 2013-08-28 
• Deposition Author(s): Stella, S., Molina, R., Yefimenko, I., Prieto, J., Silva, G.H., Bertonati, C., Juillerat, A., Duchateau, P., Montoya, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.290 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.246 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: experimental

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 D Biol Crystallogr 69: 1707

• PubMed: 23999294 
• DOI: https://doi.org/10.1107/S0907444913016429
• Primary Citation Related Structures: 
  2YPF


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 91.84 kDa 
• Atom Count: 5,822 
• Modeled Residue Count: 718 
• Deposited Residue Count: 801 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AVRBS3	A	758	Xanthomonas campestris	Mutation(s): 0
UniProt
Find proteins for Q3ZD73 (Xanthomonas campestris pv. armoraciae) Explore Q3ZD73  Go to UniProtKB:  Q3ZD73

Entity ID: 2
Molecule	Chains	Length	Organism	Image
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'	B	22	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3'	C	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.290 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.246 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 151.11	α = 90
b = 100.25	β = 102.55
c = 61.37	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-28 
Deposition Author(s): Stella, S., Molina, R., Yefimenko, I., Prieto, J., Silva, G.H., Bertonati, C., Juillerat, A., Duchateau, P., Montoya, G.

Revision History  

• Version 1.0: 2013-08-28
  Type: Initial release
  
• Version 1.1: 2013-09-11
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description