3BTS

Crystal structure of a ternary complex of the transcriptional repressor Gal80p (Gal80S0 [G301R]) and the acidic activation domain of Gal4p (aa 854-874) from Saccharomyces cerevisiae with NAD

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.175 

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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 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactose/lactose metabolism regulatory protein GAL80
A, B
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

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein GAL4C [auth E],
D [auth F]		21N/AMutation(s): 0 
UniProt
Find proteins for P04386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04386 
Go to UniProtKB:  P04386
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04386
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]		NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.071α = 90
b = 103.431β = 90
c = 106.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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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, Derived calculations
  • Version 1.3: 2023-08-30
    Changes: Data collection, Refinement description