5mC interactions in PDB entry 4GZN 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]

PDB-id

4GZN

Class

transcription-DNA

Method

X-ray (0.99 Å)

Summary

Mouse zfp57 zinc fingers in complex with methylated DNA
List of 2 5mC-amino acid contacts:

A.5CM7: other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG

B.5CM5: stacking-with-C.ARG178 is-WC-paired is-in-duplex [-]:cGC/GcG

direct SNAP output · DNAproDB 2.0

Reference

Liu, Y., Toh, H., Sasaki, H., Zhang, X., Cheng, X.: (2012) "An atomic model of Zfp57 recognition of CpG methylation within a specific DNA sequence." Genes Dev., 26, 2374-2379.

Abstract

Zinc finger transcription factor Zfp57 recognizes the methylated CpG within the TGCCGC element. We determined the structure of the DNA-binding domain of Zfp57, consisting of two adjacent zinc fingers, in complex with fully methylated DNA at 1.0 Å resolution. The first zinc finger contacts the 5' half (TGC), and the second recognizes the 3' half (CGC) of the recognition sequence. Zfp57 recognizes the two 5-methylcytosines (5mCs) asymmetrically: One involves hydrophobic interactions with Arg178, which also interacts with the neighboring 3' guanine and forms a 5mC-Arg-G interaction, while the other involves a layer of ordered water molecules. Two point mutations in patients with transient neonatal diabetes abolish DNA-binding activity. Zfp57 has reduced binding affinity for unmodified DNA and the oxidative products of 5mC.

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

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.

	No. 1 A.5CM7: download PDB file for the 5mC entry other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG
	No. 2 B.5CM5: download PDB file for the 5mC entry stacking-with-C.ARG178 is-WC-paired is-in-duplex [-]:cGC/GcG