1GD2

CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for the diversity of DNA recognition by bZIP transcription factors.

Fujii, Y.Shimizu, T.Toda, T.Yanagida, M.Hakoshima, T.

(2000) Nat Struct Biol 7: 889-893

  • DOI: 10.1038/82822
  • Primary Citation of Related Structures:  
    1GD2

  • PubMed Abstract: 
  • The basic region leucine zipper (bZIP) proteins form one of the largest families of transcription factors in eukaryotic cells. Despite relatively high homology between the amino acid sequences of the bZIP motifs, these proteins recognize diverse DNA sequences ...

    The basic region leucine zipper (bZIP) proteins form one of the largest families of transcription factors in eukaryotic cells. Despite relatively high homology between the amino acid sequences of the bZIP motifs, these proteins recognize diverse DNA sequences. Here we report the 2.0 A resolution crystal structure of the bZIP motif of one such transcription factor, PAP1, a fission yeast AP-1-like transcription factor that binds DNA containing the novel consensus sequence TTACGTAA. The structure reveals how the Pap1-specific residues of the bZIP basic region recognize the target sequence and shows that the side chain of the invariant Asn in the bZIP motif adopts an alternative conformation in Pap1. This conformation, which is stabilized by a Pap1-specific residue and its associated water molecule, recognizes a different base in the target sequence from that in other bZIP subfamilies.


    Related Citations: 
    • Crystallographic characterization of Pap1-DNA complex
      Fujii, Y., Ohira, T., Kyogoku, Y., Toda, T., Yanagida, M., Hakoshima, T.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1014

    Organizational Affiliation

    Department of Molecular Biology, Nara Institute of Science Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSCRIPTION FACTOR PAP1 EFGHIJ70Schizosaccharomyces pombeMutation(s): 0 
Find proteins for Q01663 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore Q01663 
Go to UniProtKB:  Q01663
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*GP*GP*TP*TP*AP*CP*GP*TP*AP*AP*CP*C)-3')A, B, C, D13N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.00 Å
    • R-Value Free: 0.253 
    • R-Value Work: 0.230 
    • Space Group: H 3
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 240.91α = 90
    b = 240.91β = 90
    c = 43.87γ = 120
    Software Package:
    Software NamePurpose
    MLPHAREphasing
    CNSrefinement
    DENZOdata reduction
    SCALEPACKdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-10-02
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance