6KKS

Structural insights into target DNA recognition by R2R3-type MYB transcription factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into target DNA recognition by R2R3-MYB transcription factors.

Wang, B.Luo, Q.Li, Y.Yin, L.Zhou, N.Li, X.Gan, J.Dong, A.

(2019) Nucleic Acids Res. --: --

  • DOI: 10.1093/nar/gkz1081

  • PubMed Abstract: 
  • As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the ...

    As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein, in complex with its target DNA. Structural analysis showed that the third α-helices in both the R2 and R3 repeats of WER fit in the major groove of the DNA, specifically recognizing the DNA motif 5'-AACNGC-3'. In combination with mutagenesis, in vitro binding and in vivo luciferase assays, we showed that K55, N106, K109 and N110 are critical for the function of WER. Although L59 of WER is not involved in DNA binding in the structure, ITC analysis suggested that L59 plays an important role in sensing DNA methylation at the fifth position of cytosine (5mC). Like 5mC, methylation at the sixth position of adenine (6mA) in the AAC element also inhibits the interaction between WER and its target DNA. Our study not only unravels the molecular basis of how WER recognizes its target DNA, but also suggests that 5mC and 6mA modifications may block the interaction between R2R3-MYB transcription factors and their target genes.


    Organizational Affiliation

    State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences; Institutes of Biomedical Sciences of Shanghai Medical College, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, International Associated Laboratory of CNRS-Fudan-HUNAU on Plant Epigenome Research, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.,State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, Shanghai 200438, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcription factor WER
A
119Arabidopsis thalianaMutation(s): 0 
Gene Names: WER (MYB66)
Find proteins for Q9SEI0 (Arabidopsis thaliana)
Go to UniProtKB:  Q9SEI0
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*AP*AP*TP*TP*CP*TP*CP*CP*AP*AP*CP*CP*GP*CP*AP*TP*TP*TP*TP*C)-3')B21Arabidopsis thaliana
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*AP*AP*AP*AP*TP*GP*CP*GP*GP*TP*TP*GP*GP*AP*GP*AP*AP*TP*T)-3')C21Arabidopsis thaliana
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.084α = 90.00
b = 63.927β = 90.00
c = 73.956γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2019-07-27 
  • Released Date: 2019-11-13 
  • Deposition Author(s): Wang, B., Luo, Q.

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references