6O19 | pdb_00006o19

Crystal Structure of Pho7 complex with pho1 promoter site 2

• PDB DOI: https://doi.org/10.2210/pdb6O19/pdb
• NAKB: 6O19

• Classification: TRANSCRIPTION/DNA
• Organism(s): Schizosaccharomyces pombe
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-02-18 Released: 2019-04-24 
• Deposition Author(s): Garg, A., Goldgur, Y., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

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

• PubMed: 31010807 
• DOI: https://doi.org/10.1128/MCB.00132-19
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA.
Structural Biology Program, Sloan-Kettering Institute, New York, New York, USA.
Microbiology and Immunology Department, Weill Cornell Medical College, New York, New York, USA.
Molecular Biology Program, Sloan-Kettering Institute, New York, New York, USA [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 19.16 kDa 
• Atom Count: 1,668 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor Pho7	A	59	Schizosaccharomyces pombe	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
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]	20	Schizosaccharomyces pombe

Entity ID: 3
Molecule	Chains	Length	Organism	Image
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]	20	Schizosaccharomyces pombe

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.203 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.169	α = 90
b = 37.581	β = 104.23
c = 57.564	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Garg, A., Goldgur, Y., Shuman, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R35 GM126945

Revision History  

• 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