1NK2

VND/NK-2 HOMEODOMAIN/DNA COMPLEX, NMR, 20 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Interactions of the vnd/NK-2 homeodomain with DNA by nuclear magnetic resonance spectroscopy: basis of binding specificity.

Gruschus, J.M.Tsao, D.H.Wang, L.H.Nirenberg, M.Ferretti, J.A.

(1997) Biochemistry 36: 5372-5380

  • DOI: 10.1021/bi9620060
  • Primary Citation of Related Structures:  1NK3

  • PubMed Abstract: 
  • The interactions responsible for the nucleotide sequence-specific binding of the vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding site have been identified. A three-dimensional structure of the vnd/NK-2 homeodomain-DNA com ...

    The interactions responsible for the nucleotide sequence-specific binding of the vnd/NK-2 homeodomain of Drosophila melanogaster to its consensus DNA binding site have been identified. A three-dimensional structure of the vnd/NK-2 homeodomain-DNA complex is presented, with emphasis on the structure of regions of observed protein-DNA contacts. This structure is based on protein-DNA distance restraints derived from NMR data, along with homology modeling, solvated molecular dynamics, and results from methylation and ethylation interference experiments. Helix III of the homeodomain binds in the major groove of the DNA and the N-terminal arm binds in the minor groove, in analogy with other homeodomain-DNA complexes whose structures have been reported. The vnd/NK-2 homeodomain recognizes the unusual DNA consensus sequence 5'-CAAGTG-3'. The roles in sequence specificity and strength of binding of individual amino acid residues that make contact with the DNA are described. We show, based primarily on the observed protein-DNA contacts, that the interaction of Y54 with the DNA is the major determinant of this uncommon nucleotide binding specificity in the vnd/NK-2 homeodomain-DNA complex.


    Related Citations: 
    • Elongation of Helix III of the Nk-2 Homeodomain Upon Binding to DNA: A Secondary Structure Study by NMR
      Tsao, D.H.,Gruschus, J.M.,Wang, L.H.,Nirenberg, M.,Ferretti, J.A.
      (1994) Biochemistry 33: 15053
    • Interactions of the Vnd/Nk-2 Homeodomain with DNA by Nuclear Magnetic Resonance Spectroscopy: Basis of Binding Specificity
      Gruschus, J.M.,Tsao, D.H.,Wang, L.H.,Nirenberg, M.,Ferretti, J.A.
      (1997) Biochemistry 36: 5372
    • The Three-Dimensional Solution Structure of the Nk-2 Homeodomain from Drosophila
      Tsao, D.H.,Gruschus, J.M.,Wang, L.H.,Nirenberg, M.,Ferretti, J.A.
      (1995) J.Mol.Biol. 251: 297


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, National Heart, Lung, and Blood Institute, Bethesda, Maryland 20892-0380, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HOMEOBOX PROTEIN VND
P
77Drosophila melanogasterGene Names: vnd (NK2)
Find proteins for P22808 (Drosophila melanogaster)
Go to UniProtKB:  P22808
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*GP*TP*GP*TP*CP*AP*AP*GP*TP*GP*GP*CP*TP*GP*T)-3')A16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*AP*GP*CP*CP*AP*CP*TP*TP*GP*AP*CP*AP*CP*A)-3')B16N/A
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: LEAST RESTRAINT VIOLATION 
  • Olderado: 1NK2 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance