3BTU | pdb_00003btu

Crystal structure of the super-repressor mutant of Gal80p from Saccharomyces cerevisiae; Gal80(S2) [E351K]

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 
    0.278 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.249 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3BTU

This is version 1.3 of the entry. See complete history. 

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

  • DOI: https://doi.org/10.1126/science.1151903
  • Primary Citation 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.

    • Organizational Affiliation: 
    • Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY11724, USA.

Macromolecule Content 

  • Total Structure Weight: 291.93 kDa 
  • Atom Count: 18,389 
  • Modeled Residue Count: 2,335 
  • Deposited Residue Count: 2,628 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Galactose/lactose metabolism regulatory protein GAL80
A, B, C, D, E
A, B, C, D, E, F
438Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: GAL80
UniProt
Find proteins for P04387 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04387 
Go to UniProtKB:  P04387
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04387
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free:  0.278 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.249 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 495.32α = 90
b = 84.862β = 98.9
c = 66.46γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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: 2024-02-21
    Changes: Data collection