5mC interactions in PDB entry 4QEO auto-curated with SNAP

Last updated on 2019-09-30 by Xiang-Jun Lu <xiangjun@x3dna.org>. The block schematics were created with DSSR and rendered using PyMOL.

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X-ray (2.0 Å)
Crystal structure of kryptonite in complex with mchh DNA, h3(1-15) peptide and sah
List of 1 5mC-amino acid contact:
  1. C.5CM7: stacking-with-A.TYR207 stacking-with-A.TYR219 not-WC-paired not-in-duplex
direct SNAP output · DNAproDB 2.0
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) "Mechanism of DNA Methylation-Directed Histone Methylation by KRYPTONITE." Mol.Cell, 55, 495-504.
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.

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List of 1 5mC-amino acid contact [summary · schematics · top · homepage · tutorial]

No. 1 C.5CM7: download PDB file for the 5mC entry
stacking-with-A.TYR207 stacking-with-A.TYR219 not-WC-paired not-in-duplex