6E33

Crystal Structure of Pho7-DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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This is version 2.2 of the entry. See complete history


Literature

Distinctive structural basis for DNA recognition by the fission yeast Zn2Cys6 transcription factor Pho7 and its role in phosphate homeostasis.

Garg, A.Goldgur, Y.Schwer, B.Shuman, S.

(2018) Nucleic Acids Res 46: 11262-11273

  • DOI: 10.1093/nar/gky827
  • Primary Citation of Related Structures:  
    6E33

  • PubMed Abstract: 
  • Pho7, a member of the Zn2Cys6 family of fungal transcription factors, is the key transcriptional activator underlying fission yeast phosphate homeostasis, a physiological response to phosphate starvation in which the pho1, pho84 and tgp1 genes are upregulated ...

    Pho7, a member of the Zn2Cys6 family of fungal transcription factors, is the key transcriptional activator underlying fission yeast phosphate homeostasis, a physiological response to phosphate starvation in which the pho1, pho84 and tgp1 genes are upregulated. Here, we delineated a minimized 61-amino-acid Pho7 DNA-binding domain (DBD) and determined the 1.7 Å crystal structure of the DBD at its target site in the tgp1 promoter. Two distinctive features of the Pho7 DBD are: it binds DNA as a monomer, unlike most other fungal zinc-cluster factors that bind as homodimers; and it makes extensive interactions with its asymmetric target sequence over a 14-bp footprint that entails hydrogen bonding to 13 individual bases within, and remote from, the CGG triplet typically recognized by other Zn2Cys6 DBDs. Base pair substitutions at Pho7 sites in the tgp1 and pho1 promoters highlight the importance of the 5'-CGG triplet for Pho7 binding in vitro and Pho7-dependent gene expression in vivo. We identify several DBD amino acids at which alanine substitution effaced or attenuated the pho1 phosphate starvation response and concordantly reduced Pho7 binding to a pho1 promoter site.


    Organizational Affiliation

    Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10065, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized transcriptional regulatory protein C27B12.11cA61Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: pi067SPBC27B12.11c
UniProt
Find proteins for O13658 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13658 
Go to UniProtKB:  O13658
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*CP*CP*TP*TP*CP*GP*GP*AP*CP*AP*TP*TP*CP*AP*AP*AP*TP*CP*A)-3')B [auth C]20Schizosaccharomyces pombe
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*AP*TP*TP*TP*GP*AP*AP*TP*GP*TP*CP*CP*GP*AP*AP*GP*GP*AP*T)-3')C [auth B]20Schizosaccharomyces pombe
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A], E [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.71 Å
      • R-Value Free: 0.215 
      • R-Value Work: 0.188 
      • R-Value Observed: 0.189 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 50.827α = 90
      b = 40.682β = 105.84
      c = 58.237γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      SHELXCDphasing
      Omodel building

      Structure Validation

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      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR35 GM126945

      Revision History  (Full details and data files)

      • Version 1.0: 2018-10-24
        Type: Initial release
      • Version 2.0: 2018-11-21
        Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
      • Version 2.1: 2018-12-19
        Changes: Data collection, Database references
      • Version 2.2: 2019-12-04
        Changes: Author supporting evidence