PDBsum entry 6wlh

Transcription

PDB id: 6wlh

Contents

Protein chain

118 a.a.

DNA/RNA

Metals

_ZN ×4

PDB id:

6wlh

Name:

Transcription

Title:

RNA complex of wt1 zinc finger transcription factor

Structure:

Wilms tumor protein. Chain: a. Synonym: wt33. Engineered: yes. RNA (29-mer). Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: wt1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Synthetic construct. Organism_taxid: 32630

NMR struc:

20 models

Authors:

P.E.Wright,H.J.Dyson

Key ref:

T.Nishikawa et al. (2020). RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1. Biochemistry, 59, 3889-3901. PubMed id: 32955251 DOI: 10.1021/acs.biochem.0c00602

Date:

20-Apr-20 Release date: 03-Mar-21

Protein chain

P19544  (WT1_HUMAN) -  Wilms tumor protein from Homo sapiens

Seq: 449 a.a.

Struc: 118 a.a.

DNA/RNA chain

G-G-G-C-C-A-C-C-A-A-C-G-A-C-A-U-U-G-A-U-A-U-G-G-U-G-C-C-C 29 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1021/acs.biochem.0c00602

Biochemistry 59:3889-3901 (2020)

PubMed id: 32955251

RNA Binding by the KTS Splice Variants of Wilms' Tumor Suppressor Protein WT1.

T.Nishikawa, J.M.Wojciak, H.J.Dyson, P.E.Wright.

ABSTRACT

Wilms' tumor suppressor protein WT1 regulates the expression of multiple genes through binding of the Cys₂-His₂ zinc finger domain to promoter sites. WT1 has also been proposed to be involved in post-transcriptional regulation, by binding to RNA using the same set of zinc fingers. WT1 has two major splice variants, where the Lys-Thr-Ser (KTS) tripeptide is inserted into the linker between the third and fourth zinc fingers. To obtain insights into the mechanism by which the different WT1 splice variants recognize both DNA and RNA, we have determined the solution structure of the WT1 (-KTS) zinc finger domain in complex with a 29mer stem-loop RNA. Zinc fingers 1-3 bind in a widened major groove favored by the presence of a bulge nucleotide in the double-stranded helical stem. Fingers 2 and 3 make specific contacts with the nucleobases in a conserved AUGG sequence in the helical stem. Nuclear magnetic resonance chemical shift mapping and relaxation analysis show that fingers 1-3 of the two splice variants (-KTS and +KTS) of WT1 form similar complexes with RNA. Finger 4 of the -KTS isoform interacts weakly with the RNA loop, an interaction that is abrogated in the +KTS isoform, and both isoforms bind with similar affinity to the RNA. In contrast, finger 4 is required for high-affinity binding to DNA and insertion of KTS into the linker of fingers 3 and 4 abrogates DNA binding. While finger 1 is required for RNA binding, it is dispensable for binding to consensus DNA sites.