2YPF

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

Summary for 2YPF

• Entry DOI: 10.2210/pdb2ypf/pdb
• Descriptor: AVRBS3, 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', 5'-D(*TP*AP*GP*AP*GP*GP*GP*TP*TP*AP*GP*GP*TP*TP *TP*AP*TP*AP*TP*AP*AP)-3', ... (4 entities in total)
• Functional Keywords: dna binding protein-dna complex, dna binding protein/dna
• Biological source: XANTHOMONAS CAMPESTRIS; More
• Total number of polymer chains: 3
• Total formula weight: 91839.07

Authors

Stella, S.,Molina, R.,Yefimenko, I.,Prieto, J.,Silva, G.H.,Bertonati, C.,Juillerat, A.,Duchateau, P.,Montoya, G. (deposition date: 2012-10-30, release date: 2013-08-28, Last modification date: 2023-12-20)

Primary citation

Stella, S.,Molina, R.,Yefimenko, I.,Prieto, J.,Silva, G.H.,Bertonati, C.,Juillerat, A.,Duchateau, P.,Montoya, G.
Structure of the Avrbs3-DNA Complex Provides New Insights Into the Initial Thymine-Recognition Mechanism
Acta Crystallogr.,Sect.D, 69:1707-, 2013

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.

PubMed: 23999294
DOI: 10.1107/S0907444913016429

Experimental method

X-RAY DIFFRACTION (2.55 Å)