Summary information and primary citation
- PDB-id
- 4gzn; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- transcription-DNA
- Method
- X-ray (0.99 Å)
- Summary
- Mouse zfp57 zinc fingers in complex with methylated DNA
- 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. doi: 10.1101/gad.202200.112.
- 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.
- The contacts include paired nucleotides (mostly a G in Watson-Crick G-C pairing), and
amino-acids within a 4.5-A distance cutoff to base atoms of 5mC.
- The structure is oriented in the 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: other-contacts is-WC-paired is-in-duplex [+]:CcG/cGG |
 |
|
No. 2 B.5CM5: stacking-with-C.ARG178 is-WC-paired is-in-duplex [-]:cGC/GcG |
 |
|
