1YO5

Analysis of the 2.0A crystal structure of the protein-DNA complex of human PDEF Ets domain bound to the prostate specific antigen regulatory site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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This is version 1.2 of the entry. See complete history


Literature

Analysis of the 2.0 A Crystal Structure of the Protein-DNA Complex of the Human PDEF Ets Domain Bound to the Prostate Specific Antigen Regulatory Site

Wang, Y.Feng, L.Said, M.Balderman, S.Fayazi, Z.Liu, Y.Ghosh, D.Gulick, A.M.

(2005) Biochemistry 44: 7095-7106

  • DOI: 10.1021/bi047352t
  • Primary Citation of Related Structures:  
    1YO5

  • PubMed Abstract: 
  • PDEF, a prostate epithelial specific transcription factor, is a member of the Ets family of DNA binding proteins. Here we report a 2.0 A crystal structure of the PDEF Ets domain in complex with a natural, high-affinity DNA binding site in the promoter/enhancer region of the human prostate specific antigen gene ...

    PDEF, a prostate epithelial specific transcription factor, is a member of the Ets family of DNA binding proteins. Here we report a 2.0 A crystal structure of the PDEF Ets domain in complex with a natural, high-affinity DNA binding site in the promoter/enhancer region of the human prostate specific antigen gene. Comparison of the PDEF-DNA complex with other Ets complexes revealed key features that are shared among Ets members, as well as important differences in substrate specification at both the "GGA" core and the flanking regions of the DNA site. The combination of the serine residue at position 308 and the glutamine at position 311 explains the previous observation that the PDEF binds preferentially to a thymine at the +4 position of its binding site. Despite the common essential features that are shared among Ets members, PDEF demonstrates distinct patterns of interactions at different positions of DNA in achieving sequence specific recognition. Collectively, the common and unique interactions with both the DNA bases and the backbone phosphates lead to substrate specificity and individual preference for certain DNA sites.


    Organizational Affiliation

    Hauptman Woodward Medical Institute, 73 High Street, Buffalo, New York 14203, USA. yangzhou.wang@hp.com



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
SAM pointed domain containing ets transcription factorC97Homo sapiensMutation(s): 0 
Gene Names: PDEFSPDEFPSE
UniProt & NIH Common Fund Data Resources
Find proteins for O95238 (Homo sapiens)
Explore O95238 
Go to UniProtKB:  O95238
PHAROS:  O95238
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    Enhancer site of Prostate Specific Antigen Promoter RegionA13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      Enhancer site of Prostate Specific Antigen Promoter RegionB13N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.00 Å
      • R-Value Free: 0.239 
      • R-Value Work: 0.203 
      • R-Value Observed: 0.205 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 36.16α = 90
      b = 71.476β = 113.45
      c = 39.136γ = 90
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      MOLREPphasing
      REFMACrefinement

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2005-05-17
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance