4R2E: Wilms Tumor Protein (wt1) Zinc Fingers In Complex With Methylated Dna

Citation:
Abstract
In mammalian DNA, cytosine occurs in several chemical forms, including unmodified cytosine (C), 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5mC is a major epigenetic signal that acts to regulate gene expression. 5hmC, 5fC, and 5caC are oxidized derivatives that might also act as distinct epigenetic signals. We investigated the response of the zinc finger DNA-binding domains of transcription factors early growth response protein 1 (Egr1) and Wilms tumor protein 1 (WT1) to different forms of modified cytosine within their recognition sequence, 5'-GCG(T/G)GGGCG-3'. Both displayed high affinity for the sequence when C or 5mC was present and much reduced affinity when 5hmC or 5fC was present, indicating that they differentiate primarily oxidized C from unoxidized C, rather than methylated C from unmethylated C. 5caC affected the two proteins differently, abolishing binding by Egr1 but not by WT1. We ascribe this difference to electrostatic interactions in the binding sites. In Egr1, a negatively charged glutamate conflicts with the negatively charged carboxylate of 5caC, whereas the corresponding glutamine of WT1 interacts with this group favorably. Our analyses shows that zinc finger proteins (and their splice variants) can respond in modulated ways to alternative modifications within their binding sequence.
PDB ID: 4R2EDownload
MMDB ID: 123661
PDB Deposition Date: 2014/8/11
Updated in MMDB: 2014/11
Experimental Method:
x-ray diffraction
Resolution: 1.84  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4R2E: trimeric; determined by author and by software (PISA)
Molecular Components in 4R2E
Label Count Molecule
Protein (1 molecule)
1
Wilms Tumor Protein, Isoform 4/cra_a(Gene symbol: WT1)
Molecule annotation
Nucleotides(2 molecules)
1
DNA (5'-d(*ap*gp*cp*gp*tp*gp*gp*gp*(5cm)p*gp*t)-3')
Molecule annotation
1
DNA (5'-d(*tp*ap*(5cm)p*gp*cp*cp*cp*ap*cp*gp*c)-3')
Molecule annotation
Chemicals (3 molecules)
1
3
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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