6O19

Crystal Structure of Pho7 complex with pho1 promoter site 2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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This is version 1.4 of the entry. See complete history. 


Literature

Structure of Fission Yeast Transcription Factor Pho7 Bound topho1Promoter DNA and Effect of Pho7 Mutations on DNA Binding and Phosphate Homeostasis.

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

(2019) Mol Cell Biol 39

  • DOI: https://doi.org/10.1128/MCB.00132-19
  • Primary Citation of Related Structures:  
    6O19

  • PubMed Abstract: 

    Pho7 is the Schizosaccharomyces pombe fission yeast Zn 2 Cys 6 transcriptional factor that drives a response to phosphate starvation in which phosphate acquisition genes are upregulated. Here we report a crystal structure at 1.6-Å resolution of the Pho7 DNA-binding domain (DBD) bound at its target site 2 in the pho1 promoter (5'-TCGGAAATTAAAAA). Comparison to the previously reported structure of Pho7 DBD in complex with its binding site in the tgp1 promoter (5'-TCGGACATTCAAAT) reveals shared determinants of target site specificity as well as variations in the protein-DNA interface that accommodate different promoter DNA sequences. Mutagenesis of Pho7 amino acids at the DNA interface identified nucleobase contacts at the periphery of the footprint that are essential for the induction of pho1 expression in response to phosphate starvation and for Pho7 binding to site 1 in the pho1 promoter.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor Pho759Schizosaccharomyces pombeMutation(s): 0 
Gene Names: pi067, SPBC27B12.11c
UniProt
Find proteins for O13658 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O13658 
Go to UniProtKB:  O13658
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO13658
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*TP*AP*TP*TP*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*AP*AP*CP*A)-3')B [auth C]20Schizosaccharomyces pombe
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*AP*TP*TP*TP*CP*CP*GP*AP*AP*TP*AP*AP*T)-3')C [auth B]20Schizosaccharomyces pombe
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.169α = 90
b = 37.581β = 104.23
c = 57.564γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

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: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description