3W6V

Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Complex Structure of the DNA-binding Domain of AdpA, the Global Transcription Factor in Streptomyces griseus, and a Target Duplex DNA Reveals the Structural Basis of Its Tolerant DNA Sequence Specificity

Yao, M.D.Ohtsuka, J.Nagata, K.Miyazono, K.Zhi, Y.Ohnishi, Y.Tanokura, M.

(2013) J.Biol.Chem. 288: 31019-31029

  • DOI: 10.1074/jbc.M113.473611

  • PubMed Abstract: 
  • AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with ...

    AdpA serves as the global transcription factor in the A-factor regulatory cascade, controlling the secondary metabolism and morphological differentiation of the filamentous bacterium Streptomyces griseus. AdpA binds to over 500 operator regions with the consensus sequence 5'-TGGCSNGWWY-3' (where S is G or C, W is A or T, Y is T or C, and N is any nucleotide). However, it is still obscure how AdpA can control hundreds of genes. To elucidate the structural basis of this tolerant DNA recognition by AdpA, we focused on the interaction between the DNA-binding domain of AdpA (AdpA-DBD), which consists of two helix-turn-helix motifs, and a target duplex DNA containing the consensus sequence 5'-TGGCGGGTTC-3'. The crystal structure of the AdpA-DBD-DNA complex and the mutant analysis of AdpA-DBD revealed its unique manner of DNA recognition, whereby only two arginine residues directly recognize the consensus sequence, explaining the strict recognition of G and C at positions 2 and 4, respectively, and the tolerant recognition of other positions of the consensus sequence. AdpA-DBD confers tolerant DNA sequence specificity to AdpA, allowing it to control hundreds of genes as a global transcription factor.


    Organizational Affiliation

    From the Departments of Applied Biological Chemistry and.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AdpA
A
147Streptomyces griseusGene Names: adpA
Find proteins for Q9S166 (Streptomyces griseus)
Go to UniProtKB:  Q9S166
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3')B16N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3')C16N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 76.510α = 90.00
b = 100.640β = 90.00
c = 100.910γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-11-20
    Type: Database references