Last updated on 2019-09-30 by Xiang-Jun Lu <firstname.lastname@example.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:
B.5CM5: stacking-with-A.ARG443 is-WC-paired is-in-duplex [+]:GcG/cGC
C.5CM5: other-contacts is-WC-paired is-in-duplex [-]:cGT/AcG
- 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.
- The 5-methylcytosine group (PDB ligand '5CM') is shown in space-filling model, with the methyl-carbon atom in black.
- Watson-Crick base pairs are represented as long rectangular blocks with the minor-groove edge in black. Color code: A-T red, C-G yellow, G-C green, T-A blue.
- Protein is shown as cartoon in purple. DNA backbones are shown ribbon, colored code by chain identifier.
- The block schematics were created with 3DNA-DSSR, and images were rendered using PyMOL.
- Download the PyMOL session file corresponding to the top-left image in the following panel.
List of 2 5mC-amino acid contacts [summary · schematics · top · homepage · tutorial]
- The contacts include paired nucleotides (mostly a G in G-C pairing), and amino-acids within a 4.5-A distance cutoff to the base atoms of 5mC.
- The structure is oriented in the 'standard' base reference frame of 5mC, allowing for easy comparison and direct superimposition between entries.
- The black sphere (•) denotes the 5-methyl carbon atom in 5mC.