1ZQ3

NMR Solution Structure of the Bicoid Homeodomain Bound to the Consensus DNA Binding Site TAATCC


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

The solution structure of the native K50 Bicoid homeodomain bound to the consensus TAATCC DNA-binding site.

Baird-Titus, J.M.Clark-Baldwin, K.Dave, V.Caperelli, C.A.Ma, J.Rance, M.

(2006) J.Mol.Biol. 356: 1137-1151

  • DOI: 10.1016/j.jmb.2005.12.007

  • PubMed Abstract: 
  • The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by ...

    The solution structure of the homeodomain of the Drosophila morphogenic protein Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only known protein that uses a homeodomain to regulate translation, as well as transcription, by binding to both RNA and DNA during early Drosophila development; in addition, the Bcd homeodomain can recognize an array of different DNA sites. The dual functionality and broad recognition capabilities signify that the Bcd homeodomain may possess unique structural/dynamic properties. Bicoid is the founding member of the K50 class of homeodomain proteins, containing a lysine residue at the critical 50th position (K50) of the homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also has an arginine residue at the 54th position (R54), which is essential for RNA recognition. Bcd is the only known homeodomain with the K50/R54 combination of residues. The Bcd structure indicates that this homeodomain conforms to the conserved topology of the homeodomain motif, but exhibits a significant variation from other homeodomain structures at the end of helix 1. A key result is the observation that the side-chains of the DNA-contacting residues K50, N51 and R54 all show strong signs of flexibility in the protein-DNA interface. This finding is supportive of the adaptive-recognition theory of protein-DNA interactions.


    Organizational Affiliation

    Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati College of Medicine, 231 Albert Sabin Way, Medical Sciences Building, Cincinnati, OH 45267-0524, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Homeotic bicoid protein
P
68Drosophila melanogasterMutation(s): 0 
Gene Names: bcd
Find proteins for P09081 (Drosophila melanogaster)
Go to UniProtKB:  P09081
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*TP*CP*TP*AP*AP*TP*CP*CP*CP*CP*G)-3'A13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*GP*GP*GP*AP*TP*TP*AP*GP*AP*GP*C)-3'B13N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1ZQ3 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-02-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance