2O8J

Human euchromatic histone methyltransferase 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural biology of human H3K9 methyltransferases

Wu, H.Min, J.Lunin, V.V.Antoshenko, T.Dombrovski, L.Zeng, H.Allali-Hassani, A.Campagna-Slater, V.Vedadi, M.Arrowsmith, C.H.Plotnikov, A.N.Schapira, M.

(2010) PLoS One 5: e8570-e8570

  • DOI: 10.1371/journal.pone.0008570
  • Primary Citation of Related Structures:  
    2QPW, 2R3A, 2RFI, 2O8J, 2IGQ, 3HNA

  • PubMed Abstract: 
  • SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates ...

    SET domain methyltransferases deposit methyl marks on specific histone tail lysine residues and play a major role in epigenetic regulation of gene transcription. We solved the structures of the catalytic domains of GLP, G9a, Suv39H2 and PRDM2, four of the eight known human H3K9 methyltransferases in their apo conformation or in complex with the methyl donating cofactor, and peptide substrates. We analyzed the structural determinants for methylation state specificity, and designed a G9a mutant able to tri-methylate H3K9. We show that the I-SET domain acts as a rigid docking platform, while induced-fit of the Post-SET domain is necessary to achieve a catalytically competent conformation. We also propose a model where long-range electrostatics bring enzyme and histone substrate together, while the presence of an arginine upstream of the target lysine is critical for binding and specificity.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific 3A, B, C, D281Homo sapiensMutation(s): 0 
Gene Names: EHMT2BAT8G9ANG36C6orf30KMT1C
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96KQ7 (Homo sapiens)
Explore Q96KQ7 
Go to UniProtKB:  Q96KQ7
PHAROS:  Q96KQ7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH (Subject of Investigation/LOI)
Query on SAH

Download Ideal Coordinates CCD File 
I [auth A], N [auth B], S [auth C], X [auth D]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A] , F [auth A] , G [auth A] , H [auth A] , J [auth B] , K [auth B] , L [auth B] , M [auth B] , 
E [auth A],  F [auth A],  G [auth A],  H [auth A],  J [auth B],  K [auth B],  L [auth B],  M [auth B],  O [auth C],  P [auth C],  Q [auth C],  R [auth C],  T [auth D],  U [auth D],  V [auth D],  W [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  2O8J Ki: 570 (nM) from 1 assay(s)
IC50: min: 2000, max: 4100 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.586α = 81.11
b = 70.965β = 75.13
c = 83.046γ = 88.39
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance