3V2U

Crystal structure of the yeast GAL regulon complex of the repressor, Gal80p, and the transducer, Gal3p, with galactose and ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

The Gal3p transducer of the GAL regulon interacts with the Gal80p repressor in its ligand-induced closed conformation.

Lavy, T.Kumar, P.R.He, H.Joshua-Tor, L.

(2012) Genes Dev 26: 294-303

  • DOI: https://doi.org/10.1101/gad.182691.111
  • Primary Citation of Related Structures:  
    3V2U, 3V5R

  • PubMed Abstract: 

    A wealth of genetic information and some biochemical analysis have made the GAL regulon of the yeast Saccharomyces cerevisiae a classic model system for studying transcriptional activation in eukaryotes. Galactose induces this transcriptional switch, which is regulated by three proteins: the transcriptional activator Gal4p, bound to DNA; the repressor Gal80p; and the transducer Gal3p. We showed previously that NADP appears to act as a trigger to kick the repressor off the activator. Sustained activation involves a complex of the transducer Gal3p and Gal80p mediated by galactose and ATP. We solved the crystal structure of the complex of Gal3p-Gal80p with α-D-galactose and ATP to 2.1 Å resolution. The interaction between the proteins occurs only when Gal3p is in a "closed" state induced by ligand binding. The structure of the complex provides a rationale for the phenotypes of several well-known Gal80p and Gal3p mutants as well as the lack of galactokinase activity of Gal3p.


  • Organizational Affiliation

    Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Galactose/lactose metabolism regulatory protein GAL80
A, B
438Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GAL80YML051WYM9958.12YM9827.01
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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein GAL3
C, D
520Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: GAL3YDR009WYD8119.14
UniProt
Find proteins for P13045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13045 
Go to UniProtKB:  P13045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13045
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
I [auth C],
L [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
GLA
Query on GLA

Download Ideal Coordinates CCD File 
H [auth C],
K [auth D]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth C],
J [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.186α = 114.04
b = 83.221β = 92.88
c = 92.629γ = 90.37
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2012-03-14
    Changes: Refinement description
  • Version 1.2: 2012-03-21
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Refinement description, Structure summary