5T0M

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading

  • Classification: TRANSFERASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2016-08-16 Released: 2016-10-05 
  • Deposition Author(s): Xu, K., Tong, L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/Office of the Director; National Institutes of Health/National Center for Research Resources 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.896 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A histone H3K9M mutation traps histone methyltransferase Clr4 to prevent heterochromatin spreading.

Shan, C.M.Wang, J.Xu, K.Chen, H.Yue, J.X.Andrews, S.Moresco, J.J.Yates, J.R.Nagy, P.L.Tong, L.Jia, S.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.17903
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms of function are controver ...

    Histone lysine-to-methionine (K-to-M) mutations are associated with multiple cancers, and they function in a dominant fashion to block the methylation of corresponding lysines on wild type histones. However, their mechanisms of function are controversial. Here we show that in fission yeast, introducing the K9M mutation into one of the three histone H3 genes dominantly blocks H3K9 methylation on wild type H3 across the genome. In addition, H3K9M enhances the interaction of histone H3 tail with the H3K9 methyltransferase Clr4 in a SAM (S-adenosyl-methionine)-dependent manner, and Clr4 is trapped at nucleation sites to prevent its spreading and the formation of large heterochromatin domains. We further determined the crystal structure of an H3K9M peptide in complex with human H3K9 methyltransferase G9a and SAM, which reveales that the methionine side chain had enhanced van der Waals interactions with G9a. Therefore, our results provide a detailed mechanism by which H3K9M regulates H3K9 methylation.


    Organizational Affiliation

    Department of Pathology, Columbia University, New York, United States.,Institute for Research on Cancer and Aging, Nice (IRCAN), CNRS UMR 7284, INSERM U1081, Nice, France.,Department of Biological Sciences, Columbia University, New York, United States.,Department of Chemical Physiology, Scripps Research Institute, La Jolla, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase EHMT2
A, B
281Homo sapiensMutation(s): 0 
Gene Names: EHMT2 (BAT8, C6orf30, G9A, KMT1C, NG36)
EC: 2.1.1.-, 2.1.1.43
Find proteins for Q96KQ7 (Homo sapiens)
Go to Gene View: EHMT2
Go to UniProtKB:  Q96KQ7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THR-LYS-GLN-THR-ALA-ARG-NLE-SER-THR-GLY
P, C
15Homo sapiensMutation(s): 0 
Gene Names: H3C1, H3C2, H3C3, H3C4, H3C6, H3C7, H3C8, H3C10, H3C11, H3C12 (H3FA, HIST1H3A, H3FL, HIST1H3B, H3FC HIST1H3C, H3FB, HIST1H3D, H3FD, HIST1H3E, H3FI, HIST1H3F, H3FH, HIST1H3G, H3FK, HIST1H3H, H3FF, HIST1H3I, H3FJ, HIST1H3J)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

Download SDF File 
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
SAM
Query on SAM

Download SDF File 
Download CCD File 
A, B
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
C, P
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.896 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.623α = 90.00
b = 78.284β = 91.16
c = 71.803γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-16 
  • Released Date: 2016-10-05 
  • Deposition Author(s): Xu, K., Tong, L.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM085145
National Institutes of Health/Office of the DirectorUnited StatesS10-OD012018
National Institutes of Health/National Center for Research ResourcesUnited StatesP41-RR011823
National Institutes of Health/National Institute of General Medical SciencesUnited StatesP41-GM103533

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Derived calculations