1GD2

CRYSTAL STRUCTURE OF BZIP TRANSCRIPTION FACTOR PAP1 BOUND TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 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.Mol.Biol. 7: 889-893

  • DOI: 10.1038/82822

  • 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 ...

    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.,Sect.D 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: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TRANSCRIPTION FACTOR PAP1
E, F, G, H, I, J
70Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: pap1 (caf3)
Find proteins for Q01663 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q01663
Entity ID: 1
MoleculeChainsLengthOrganism
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 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.230 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 240.910α = 90.00
b = 240.910β = 90.00
c = 43.870γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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