4QEN

crystal structure of KRYPTONITE in complex with mCHH DNA and SAH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 

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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:  
    4QEN, 4QEO, 4QEP

  • 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 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 ...

    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 LengthOrganismDetailsImage
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)
UniProt
Find proteins for Q8GZB6 (Arabidopsis thaliana)
Explore Q8GZB6 
Go to UniProtKB:  Q8GZB6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GZB6
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM)P*AP*TP*CP*AP*GP*TP*AP*T)-3')B [auth C]15N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (5'-D(*AP*CP*TP*GP*AP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)-3')C [auth D]15N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
D [auth A]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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.395α = 90
b = 98.009β = 90
c = 122.581γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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