2QPW

Methyltransferase domain of human PR domain-containing protein 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 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:  

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PR domain zinc finger protein 2
A
149Homo sapiensMutation(s): 0 
Gene Names: PRDM2 (KMT8, RIZ)
EC: 2.1.1.43
Find proteins for Q13029 (Homo sapiens)
Go to Gene View: PRDM2
Go to UniProtKB:  Q13029
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.462α = 90.00
b = 51.196β = 90.00
c = 70.887γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
HKL-2000data scaling
ADSCdata collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2007-08-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance