4QEP: Crystal Structure Of Kryptonite In Complex With Mchg Dna And Sah

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 epsilon-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.
PDB ID: 4QEPDownload
MMDB ID: 121968
PDB Deposition Date: 2014/5/17
Updated in MMDB: 2014/08
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4QEP: trimeric; determined by author and by software (PISA)
Molecular Components in 4QEP
Label Count Molecule
Protein (1 molecule)
Histone-lysine N-methyltransferase, H3 Lysine-9 Specific Suvh4(Gene symbol: SUVH4)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*gp*gp*tp*ap*cp*tp*(5cm) P*ap*gp*cp*ap*gp*tp*ap*t)-3')
Molecule annotation
DNA (5'-d(*ap*cp*tp*gp*cp*tp*gp*ap*gp*tp*ap*cp*cp*ap*t)- 3')
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB