5CC1

S425G Glucocorticoid receptor DNA binding domain - (+)GRE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space.

Hudson, W.H.Kossmann, B.R.de Vera, I.M.Chuo, S.W.Weikum, E.R.Eick, G.N.Thornton, J.W.Ivanov, I.N.Kojetin, D.J.Ortlund, E.A.

(2016) Proc.Natl.Acad.Sci.USA 113: 326-331

  • DOI: 10.1073/pnas.1518960113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many genomes contain families of paralogs--proteins with divergent function that evolved from a common ancestral gene after a duplication event. To understand how paralogous transcription factors evolve divergent DNA specificities, we examined how th ...

    Many genomes contain families of paralogs--proteins with divergent function that evolved from a common ancestral gene after a duplication event. To understand how paralogous transcription factors evolve divergent DNA specificities, we examined how the glucocorticoid receptor and its paralogs evolved to bind activating response elements [(+)GREs] and negative glucocorticoid response elements (nGREs). We show that binding to nGREs is a property of the glucocorticoid receptor (GR) DNA-binding domain (DBD) not shared by other members of the steroid receptor family. Using phylogenetic, structural, biochemical, and molecular dynamics techniques, we show that the ancestral DBD from which GR and its paralogs evolved was capable of binding both nGRE and (+)GRE sequences because of the ancestral DBD's ability to assume multiple DNA-bound conformations. Subsequent amino acid substitutions in duplicated daughter genes selectively restricted protein conformational space, causing this dual DNA-binding specificity to be selectively enhanced in the GR lineage and lost in all others. Key substitutions that determined the receptors' response element-binding specificity were far from the proteins' DNA-binding interface and interacted epistatically to change the DBD's function through DNA-induced allosteric mechanisms. These amino acid substitutions subdivided both the conformational and functional space of the ancestral DBD among the present-day receptors, allowing a paralogous family of transcription factors to control disparate transcriptional programs despite high sequence identity.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322;




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B, W, X
114Homo sapiensMutations: S33G
Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')C,Z18synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')D,Y18synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, W, X
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.302 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.245 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 176.721α = 90.00
b = 39.122β = 101.10
c = 132.099γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
SERGUIdata collection
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney DiseaseUnited StatesR01DK095750
American Heart AssociationUnited States14GRNT20460124
American Heart AssociationUnited States13PRE16920012

Revision History 

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-03-16
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence, Database references, Derived calculations