5TQR

ctPRC2 in an autoinhibited conformation bound to S-adenosylmethionine

  • Classification: TRANSFERASE
  • Organism(s): Thermochaetoides thermophila
  • Expression System: Saccharomyces cerevisiae
  • Mutation(s): No 

  • Deposited: 2016-10-24 Released: 2017-06-14 
  • Deposition Author(s): Bratkowski, M.A., Liu, X.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Cancer Prevention and Research Institute of Texas (CPRIT), Rita Allen Foundation, UT Southwestern Medical Center Endowed Scholar Fund

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Polycomb repressive complex 2 in an autoinhibited state.

Bratkowski, M.Yang, X.Liu, X.

(2017) J Biol Chem 292: 13323-13332

  • DOI: https://doi.org/10.1074/jbc.M117.787572
  • Primary Citation of Related Structures:  
    5BJS, 5TQR, 5VK3

  • PubMed Abstract: 

    Polycomb-group proteins control many fundamental biological processes, such as anatomical development in mammals and vernalization in plants. Polycomb repressive complex 2 (PRC2) is responsible for methylation of histone H3 lysine 27 (H3K27), and trimethylated H3K27 (H3K27me3) is implicated in epigenetic gene silencing. Recent genomic, biochemical, and structural data indicate that PRC2 is broadly conserved from yeast to human in many aspects. Here, we determined the crystal structure of an apo-PRC2 from the fungus Chaetomium thermophilum captured in a bona fide autoinhibited state, which represents a novel conformation of PRC2 associated with enzyme regulation in light of the basal and stimulated states that we reported previously. We found that binding by the cofactor S -adenosylmethionine mitigates this autoinhibited structural state. Using steady-state enzyme kinetics, we also demonstrated that disrupting the autoinhibition results in a vastly activated enzyme complex. Autoinhibition provides a novel structural platform that may enable control of PRC2 activity in response to diverse transcriptional states and chromatin contexts and set a ground state to allow PRC2 activation by other cellular mechanisms as well.


  • Organizational Affiliation

    From the Cecil H. and Ida Green Center for Reproductive Biology Sciences and Division of Basic Research, Department of Obstetrics and Gynecology, Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas 75390.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polycomb Protein EED605Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0029920
UniProt
Find proteins for G0S8H7 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S8H7 
Go to UniProtKB:  G0S8H7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S8H7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EZH2, Polycomb protein SUZ12937Thermochaetoides thermophilaMutation(s): 0 
Gene Names: CTHT_0053230CTHT_0006210
EC: 2.1.1.356
UniProt
Find proteins for G0RYC6 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0RYC6 
Go to UniProtKB:  G0RYC6
Find proteins for G0SDW4 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0SDW4 
Go to UniProtKB:  G0SDW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsG0RYC6G0SDW4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAM
Query on SAM

Download Ideal Coordinates CCD File 
K [auth B]S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth B]
D [auth B]
E [auth B]
F [auth B]
G [auth B]
C [auth B],
D [auth B],
E [auth B],
F [auth B],
G [auth B],
H [auth B],
I [auth B],
J [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.177 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.454α = 90
b = 138.008β = 90
c = 223.063γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing
Cootmodel building
HKL-3000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM114576
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM121662
Welch FoundationUnited StatesI-1790
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesR1119
Rita Allen FoundationUnited States--
UT Southwestern Medical Center Endowed Scholar FundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-14
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description