4QEN

crystal structure of KRYPTONITE in complex with mCHH DNA and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE.

Du, J.Johnson, L.M.Groth, M.Feng, S.Hale, C.J.Li, S.Vashisht, A.A.Gallego-Bartolome, J.Wohlschlegel, J.A.Patel, D.J.Jacobsen, S.E.

(2014) Mol.Cell 55: 495-504

  • DOI: 10.1016/j.molcel.2014.06.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure ...

    In Arabidopsis, CHG DNA methylation is controlled by the H3K9 methylation mark through a self-reinforcing loop between DNA methyltransferase CHROMOMETHYLASE3 (CMT3) and H3K9 histone methyltransferase KRYPTONITE/SUVH4 (KYP). We report on the structure of KYP in complex with methylated DNA, substrate H3 peptide, and cofactor SAH, thereby defining the spatial positioning of the SRA domain relative to the SET domain. The methylated DNA is bound by the SRA domain with the 5mC flipped out of the DNA, while the H3(1-15) peptide substrate binds between the SET and post-SET domains, with the ε-ammonium of K9 positioned adjacent to bound SAH. These structural insights, complemented by functional data on key mutants of residues lining the 5mC and H3K9-binding pockets within KYP, establish how methylated DNA recruits KYP to the histone substrate. Together, the structures of KYP and previously reported CMT3 complexes provide insights into molecular mechanisms linking DNA and histone methylation.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.,Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095, USA.,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, CA 90095, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4
A
533Arabidopsis thalianaMutation(s): 0 
Gene Names: SUVH4 (KYP, SDG33, SET33)
EC: 2.1.1.43
Find proteins for Q8GZB6 (Arabidopsis thaliana)
Go to UniProtKB:  Q8GZB6
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3')C15N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')D15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CM
Query on 5CM
C
DNA LINKINGC10 H16 N3 O7 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.002 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.395α = 90.00
b = 98.009β = 90.00
c = 122.581γ = 90.00
Software Package:
Software NamePurpose
PHENIXmodel building
PHENIXrefinement
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-30
    Type: Initial release
  • Version 1.1: 2014-08-20
    Type: Database references