4FT4

crystal structure of Zea mays ZMET2 in complex H3(1-32)K9me2 peptide and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Dual Binding of Chromomethylase Domains to H3K9me2-Containing Nucleosomes Directs DNA Methylation in Plants.

Du, J.Zhong, X.Bernatavichute, Y.V.Stroud, H.Feng, S.Caro, E.Vashisht, A.A.Terragni, J.Chin, H.G.Tu, A.Hetzel, J.Wohlschlegel, J.A.Pradhan, S.Patel, D.J.Jacobsen, S.E.

(2012) Cell 151: 167-180

  • DOI: 10.1016/j.cell.2012.07.034
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. H ...

    DNA methylation and histone modification exert epigenetic control over gene expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 dimethylation (H3K9me2), but the mechanism underlying this relationship is poorly understood. Here, we report multiple lines of evidence that CMT3 interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly perfectly correlated with H3K9me2, and CMT3 stably associated with H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo adjacent homology (BAH) and chromo domains. The structures reveal an aromatic cage within both BAH and chromo domains as interaction interfaces that capture H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to nucleosomes and show a complete loss of CMT3 activity in vivo. Our study establishes dual recognition of H3K9me2 marks by BAH and chromo domains and reveals a distinct mechanism of interplay between DNA methylation and histone modification.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 1
B, A
784Zea maysMutation(s): 0 
Gene Names: MET2A
EC: 2.1.1.37
Find proteins for Q9AXT8 (Zea mays)
Go to UniProtKB:  Q9AXT8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3(1-32)K9me2 peptide
P, Q
32Arabidopsis thalianaMutation(s): 0 
Gene Names: HTR2, HTR3, HTR13, HTR9, HTR1
Find proteins for P59226 (Arabidopsis thaliana)
Go to UniProtKB:  P59226
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLY
Query on MLY
P, Q
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.645α = 90.00
b = 111.558β = 101.98
c = 151.480γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
PHENIXphasing
PHENIXmodel building
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-06-27 
  • Released Date: 2012-10-17 
  • Deposition Author(s): Du, J., Patel, D.J.

Revision History 

  • Version 1.0: 2012-10-17
    Type: Initial release