5mC interactions in PDB entry 4M9E 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.

Summary information and primary citation [schematics · contacts · top · homepage · tutorial]

X-ray (1.85 Å)
Structure of klf4 zinc finger DNA binding domain in complex with methylated DNA
List of 2 5mC-amino acid contacts:
  1. B.5CM5: stacking-with-A.ARG443 is-WC-paired is-in-duplex [+]:GcG/cGC
  2. C.5CM5: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
direct SNAP output · DNAproDB 2.0
Liu, Y., Olanrewaju, Y.O., Zheng, Y., Hashimoto, H., Blumenthal, R.M., Zhang, X., Cheng, X.: (2014) "Structural basis for Klf4 recognition of methylated DNA." Nucleic Acids Res., 42, 4859-4867.
Transcription factor Krüppel-like factor 4 (Klf4), one of the factors directing cellular reprogramming, recognizes the CpG dinucleotide (whether methylated or unmodified) within a specific G/C-rich sequence. The binding affinity of the mouse Klf4 DNA-binding domain for methylated DNA is only slightly stronger than that for an unmodified oligonucleotide. The structure of the C-terminal three Krüppel-like zinc fingers (ZnFs) of mouse Klf4, in complex with fully methylated DNA, was determined at 1.85 Å resolution. An arginine and a glutamate interact with the methyl group. By comparison with two other recently characterized structures of ZnF protein complexes with methylated DNA, we propose a common principle of recognition of methylated CpG by C2H2 ZnF proteins, which involves a spatially conserved Arg-Glu pair.

Base-block schematics in six views [summary · contacts · top · homepage · tutorial]

List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]

No. 1 B.5CM5: download PDB file for the 5mC entry
stacking-with-A.ARG443 is-WC-paired is-in-duplex [+]:GcG/cGC
No. 2 C.5CM5: download PDB file for the 5mC entry
other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG