6Z2A

Structure of Clr4 mutant - F256A/F310A/F427A bound to SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

SUV39 SET domains mediate crosstalk of heterochromatic histone marks.

Stirpe, A.Guidotti, N.Northall, S.J.Kilic, S.Hainard, A.Vadas, O.Fierz, B.Schalch, T.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.62682
  • Primary Citation of Related Structures:  
    6Z2A

  • PubMed Abstract: 

    The SUV39 class of methyltransferase enzymes deposits histone H3 lysine 9 di- and trimethylation (H3K9me2/3), the hallmark of constitutive heterochromatin. How these enzymes are regulated to mark specific genomic regions as heterochromatic is poorly understood. Clr4 is the sole H3K9me2/3 methyltransferase in the fission yeast Schizosaccharomyces pombe, and recent evidence suggests that ubiquitination of lysine 14 on histone H3 (H3K14ub) plays a key role in H3K9 methylation. However, the molecular mechanism of this regulation and its role in heterochromatin formation remain to be determined. Our structure-function approach shows that the H3K14ub substrate binds specifically and tightly to the catalytic domain of Clr4, and thereby stimulates the enzyme by over 250-fold. Mutations that disrupt this mechanism lead to a loss of H3K9me2/3 and abolish heterochromatin silencing similar to clr4 deletion. Comparison with mammalian SET domain proteins suggests that the Clr4 SET domain harbors a conserved sensor for H3K14ub, which mediates licensing of heterochromatin formation.


  • Organizational Affiliation

    Department of Molecular Biology, Faculty of Science, University of Geneva, Geneva, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific296Schizosaccharomyces pombe 972h-Mutation(s): 3 
Gene Names: clr4kmt1SPBC428.08c
EC: 2.1.1.355
UniProt
Find proteins for O60016 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O60016 
Go to UniProtKB:  O60016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60016
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific294Schizosaccharomyces pombe 972h-Mutation(s): 3 
Gene Names: clr4kmt1SPBC428.08c
EC: 2.1.1.355
UniProt
Find proteins for O60016 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O60016 
Go to UniProtKB:  O60016
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60016
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
G [auth A],
M [auth B]
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
I [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.46 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.239 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.444α = 90
b = 110.288β = 90
c = 70.684γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
STARANISOdata scaling
MOLREPphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerlandPP00P3_139137
Swiss National Science FoundationSwitzerlandPP00P3_163760_1
Swiss National Science FoundationSwitzerlandPP00P3_172904

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-12-08
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Refinement description