3BTV

Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S0)-[G301R]

• PDB DOI: https://doi.org/10.2210/pdb3BTV/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-12-31 Released: 2008-03-04 
• Deposition Author(s): Kumar, P.R., Joshua-Tor, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 

Starting Model: experimental

Literature

NADP regulates the yeast GAL induction system.

Kumar, P.R., Yu, Y., Sternglanz, R., Johnston, S.A., Joshua-Tor, L.

(2008) Science 319: 1090-1092

• PubMed: 18292341 
• DOI: https://doi.org/10.1126/science.1151903
• Primary Citation of Related Structures:  
  3BTS, 3BTU, 3BTV


• PubMed Abstract: 
  

  Transcriptional regulation of the galactose-metabolizing genes in Saccharomyces cerevisiae depends on three core proteins: Gal4p, the transcriptional activator that binds to upstream activating DNA sequences (UAS(GAL)); Gal80p, a repressor that binds to the carboxyl terminus of Gal4p and inhibits transcription; and Gal3p, a cytoplasmic transducer that, upon binding galactose and adenosine 5'-triphosphate, relieves Gal80p repression. The current model of induction relies on Gal3p sequestering Gal80p in the cytoplasm. However, the rapid induction of this system implies that there is a missing factor. Our structure of Gal80p in complex with a peptide from the carboxyl-terminal activation domain of Gal4p reveals the existence of a dinucleotide that mediates the interaction between the two. Biochemical and in vivo experiments suggests that nicotinamide adenine dinucleotide phosphate (NADP) plays a key role in the initial induction event.

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Organizational Affiliation: 

Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY11724, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 97.51 kDa 
• Atom Count: 6,380 
• Modelled Residue Count: 782 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Galactose/lactose metabolism regulatory protein GAL80	A, B	438	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: GAL80
UniProt
Find proteins for P04387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04387  Go to UniProtKB:  P04387

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.215 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.087	α = 90
b = 103.947	β = 90
c = 106.179	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-04 
Deposition Author(s): Kumar, P.R., Joshua-Tor, L.

Revision History  

• Version 1.0: 2008-03-04
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description