2GLO

Solution structure of the Brinker DNA binding domain in complex with the omb enhancer


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

DNA recognition by the brinker repressor - an extreme case of coupling between binding and folding

Cordier, F.Hartmann, B.Rogowski, M.Affolter, M.Grzesiek, S.

(2006) J.Mol.Biol. 361: 659-672

  • DOI: 10.1016/j.jmb.2006.06.045

  • PubMed Abstract: 
  • The Brinker (Brk) nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signaling pathway. Its N-terminal part has weak homology to the Antennapedia homeodomain and binds to GC-rich DNA sequences. We have investigated the c ...

    The Brinker (Brk) nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signaling pathway. Its N-terminal part has weak homology to the Antennapedia homeodomain and binds to GC-rich DNA sequences. We have investigated the conformation and dynamics of the N-terminal 101 amino acid residues of Brk in the absence and in the presence of cognate DNA by solution NMR spectroscopy. In the absence of DNA, Brk is unfolded and highly flexible throughout the entire backbone. Addition of cognate DNA induces the formation of a well-folded structure for residues R46 to R95. This structure consists of four helices forming a helix-turn-helix motif that differs from homeodomains, but has similarities to the Tc3 transposase, the Pax-6 Paired domain, and the human centromere-binding protein. The GC-rich DNA recognition can be explained by specific major groove hydrogen bonds from the N-terminal end of helix alpha3. The transition from a highly flexible, completely unfolded conformation in the absence of DNA to a well-formed structure in the complex presents a very extreme case of the "coupling of binding and folding" phenomenon.


    Organizational Affiliation

    Division of Structural Biology, Biozentrum der Universit├Ąt Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
brinker CG9653-PA
A
59Drosophila melanogasterMutation(s): 0 
Gene Names: brk (brinker, BRK, Brk, brk-RA, Dm brk, Dmel\CG9653, ssg-1)
Find proteins for Q9XTN4 (Drosophila melanogaster)
Go to UniProtKB:  Q9XTN4
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*TP*GP*AP*GP*GP*CP*GP*TP*CP*AP*AP*C)-3'B12N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*TP*TP*GP*AP*CP*GP*CP*CP*TP*CP*A)-3'C12N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 2GLO Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance