PDBsum entry 4r2q

DNA binding protein/DNA

PDB id: 4r2q

Contents

Protein chain

88 a.a.

DNA/RNA

Ligands

EDO

Metals

_ZN ×3

Waters ×183

PDB id:

4r2q

Name:

DNA binding protein/DNA

Title:

Wilms tumor protein (wt1) zinc fingers in complex with formylated DNA

Structure:

Wilms tumor protein, isoform 4/cra_a. Chain: a. Fragment: zinc finger 2-4. Synonym: wt33. Engineered: yes. DNA (5'-d( Ap Gp Cp Gp Tp Gp Gp Gp (5Fc)p Gp T)-3'). Chain: b. Engineered: yes. DNA (5'-d( Tp Ap (5Fc)p Gp Cp Cp Cp Ap Cp Gp C)-3').

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: wt1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Resolution:

1.54Å R-factor: 0.162 R-free: 0.193

Authors:

H.Hashimoto,Y.O.Olanrewaju,Y.Zheng,G.G.Wilson,X.Zhang,X.Cheng

Key ref:

H.Hashimoto et al. (2014). Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence. Genes Dev, 28, 2304-2313. PubMed id: 25258363 DOI: 10.1101/gad.250746.114

Date:

12-Aug-14 Release date: 08-Oct-14

Protein chain

P19544  (WT1_HUMAN) -  Wilms tumor protein from Homo sapiens

Seq: 449 a.a.

Struc: 88 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DNA/RNA chains

A-G-C-G-T-G-G-G-5FC-G-T 11 bases

T-A-5FC-G-C-C-C-A-C-G-C 11 bases

DOI no: 10.1101/gad.250746.114

Genes Dev 28:2304-2313 (2014)

PubMed id: 25258363

Wilms tumor protein recognizes 5-carboxylcytosine within a specific DNA sequence.

H.Hashimoto, Y.O.Olanrewaju, Y.Zheng, G.G.Wilson, X.Zhang, X.Cheng.

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.