4QEO

crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

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
  • Structures With Same Primary Citation

  • 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.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH4A533Arabidopsis thalianaMutation(s): 0 
Gene Names: SUVH4KYPSDG33SET33At5g13960MAC12.7
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
Find proteins for Q8GZB6 (Arabidopsis thaliana)
Explore Q8GZB6 
Go to UniProtKB:  Q8GZB6
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Histone H3P15Xenopus laevisMutation(s): 0 
Find proteins for P84233 (Xenopus laevis)
Explore P84233 
Go to UniProtKB:  P84233
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsLengthOrganism
DNA 5'-GGTACT(5CM)ATCAGTAT-3'C15N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA 5'-ACTGATGAGTACCAT-3'D15N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.46α = 90
b = 96.765β = 90
c = 122.411γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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