5JIN

Structure of G9a SET-domain with Histone H3K9M mutant peptide and bound S-adenosylmethionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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Literature

S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3.

Jayaram, H.Hoelper, D.Jain, S.U.Cantone, N.Lundgren, S.M.Poy, F.Allis, C.D.Cummings, R.Bellon, S.Lewis, P.W.

(2016) Proc Natl Acad Sci U S A 113: 6182-6187

  • DOI: 10.1073/pnas.1605523113
  • Primary Citation of Related Structures:  
    5JHN, 5JJ0, 5JIN, 5JIY

  • PubMed Abstract: 
  • Lysine to methionine (K-to-M) mutations in genes encoding histone H3 are thought to drive a subset of pediatric brain and bone cancers. These high-frequency K-to-M mutations occur at sites of methylation on histone H3, and tumors containing the mutant histones exhibit a global loss of specific histone methylation marks ...

    Lysine to methionine (K-to-M) mutations in genes encoding histone H3 are thought to drive a subset of pediatric brain and bone cancers. These high-frequency K-to-M mutations occur at sites of methylation on histone H3, and tumors containing the mutant histones exhibit a global loss of specific histone methylation marks. Previous studies showed that K-to-M mutant histones, also known as oncohistones, are potent orthosteric inhibitors of specific Su(var)3-9, Enhancer-of-zeste, Trithorax (SET) domain methyltransferases. However, the biochemical and biophysical details of the interaction between K-to-M mutant histones and the respective SET domain methyltransferases are currently unknown. Here, we use the histone H3K9-directed methyltransferase G9a as a model to explore the mechanism of inhibition by K-to-M oncohistones. X-ray cocrystal structures revealed that the K9M residue of histone H3 occupies the active site cavity of G9a, and kinetic analysis indicates competitive inhibition of G9a by histone H3K9M. Additionally, we find that the cofactor S-adenosyl methionine (SAM) is necessary for stable interaction between G9a and H3K9M histone. Consistent with the formation of a ternary complex, we find that the inhibitory peptide is uncompetitive with regard to SAM. These data and others indicate that K-to-M oncohistones promote global loss of specific lysine methylation through sequestration and inhibition of SAM-bound SET domain methyltransferases.


    Organizational Affiliation

    Wisconsin Institute of Discovery, University of Wisconsin, Madison, WI 53715; Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715; alliscd@rockefeller.edu Richard.Cummings@constellationpharma.com Steve.Bellon@constellationpharma.com plewis@discovery.wisc.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase EHMT2A, C [auth B]274Homo sapiensMutation(s): 0 
Gene Names: EHMT2BAT8C6orf30G9AKMT1CNG36
EC: 2.1.1 (PDB Primary Data), 2.1.1.43 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.1 peptide with K9M mutationB [auth F], D [auth G]11Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.434α = 90
b = 78.684β = 90.69
c = 72.769γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-06
    Type: Initial release