PDBsum entry 2prt

Transcription/DNA

PDB id: 2prt

Contents

Protein chain

115 a.a. *

DNA/RNA

Metals

_ZN ×4

* Residue conservation analysis

PDB id:

2prt

Name:

Transcription/DNA

Title:

Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA

Structure:

DNA (5'-d( Cp Gp Cp Gp Gp Gp Gp Gp Cp Gp Tp Cp Tp G)-3'). Chain: b. Engineered: yes. DNA (5'-d( Cp Ap Gp Ap Cp Gp Cp Cp Cp Cp Cp Gp Cp G)-3'). Chain: c. Engineered: yes. Wilms tumor 1. Chain: a. Fragment: residues 174-291.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: wt1. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

3.15Å R-factor: 0.236 R-free: 0.277

Authors:

R.Stoll,B.M.Lee,E.W.Debler,J.H.Laity,I.A.Wilson,H.J.Dyson,P.E.Wright

Key ref:

R.Stoll et al. (2007). Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA. J Mol Biol, 372, 1227-1245. PubMed id: 17716689 DOI: 10.1016/j.jmb.2007.07.017

Date:

04-May-07 Release date: 04-Mar-08

Protein chain

P19544  (WT1_HUMAN) -  Wilms tumor protein from Homo sapiens

Seq: 449 a.a.

Struc: 115 a.a.

DNA/RNA chains

C-G-C-G-G-G-G-G-C-G-T-C 12 bases

C-A-G-A-C-G-C-C-C-C-C-G-C-G 14 bases

DOI no: 10.1016/j.jmb.2007.07.017

J Mol Biol 372:1227-1245 (2007)

PubMed id: 17716689

Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA.

R.Stoll, B.M.Lee, E.W.Debler, J.H.Laity, I.A.Wilson, H.J.Dyson, P.E.Wright.

ABSTRACT

The zinc finger domain of the Wilms tumor suppressor protein (WT1) contains four canonical Cys(2)His(2) zinc fingers. WT1 binds preferentially to DNA sequences that are closely related to the EGR-1 consensus site. We report the structure determination by both X-ray crystallography and NMR spectroscopy of the WT1 zinc finger domain in complex with DNA. The X-ray structure was determined for the complex with a cognate 14 base-pair oligonucleotide, and composite X-ray/NMR structures were determined for complexes with both the 14 base-pair and an extended 17 base-pair DNA. This combined approach allowed unambiguous determination of the position of the first zinc finger, which is influenced by lattice contacts in the crystal structure. The crystal structure shows the second, third and fourth zinc finger domains inserted deep into the major groove of the DNA where they make base-specific interactions. The DNA duplex is distorted in the vicinity of the first zinc finger, with a cytidine twisted and tilted out of the base stack to pack against finger 1 and the tip of finger 2. By contrast, the composite X-ray/NMR structures show that finger 1 continues to follow the major groove in the solution complexes. However, the orientation of the helix is non-canonical, and the fingertip and the N terminus of the helix project out of the major groove; as a consequence, the zinc finger side-chains that are commonly involved in base recognition make no contact with the DNA. We conclude that finger 1 helps to anchor WT1 to the DNA by amplifying the binding affinity although it does not contribute significantly to binding specificity. The structures provide molecular level insights into the potential consequences of mutations in zinc fingers 2 and 3 that are associated with Denys-Drash syndrome and nephritic syndrome. The mutations are of two types, and either destabilize the zinc finger structure or replace key base contact residues.

Selected figure(s)

Figure 5.
Figure 5. Close-up view of contacts observed in the X-ray crystal structure. (a) Interactions between Arg394 (dark blue) and Asp396 (red) of finger 3 (pink) and the bases of GUA7 (gray) and CYT29 (green) of the 14 bp DNA duplex. (b) Interactions between Arg366 (dark blue) of finger 2 (blue-green) and the bases of ADE26 (red), CYT9 (purple), GUA10 (light blue) and THY11 (green).

Figure 10.
Figure 10. Stereo view of a superposition of the X-ray structure (colors as for Figure 2), the NMR/X-ray solution structure of zf1-4 with the 14 bp DNA duplex (colors medium blue, medium blue-green, maroon and tan for fingers 1–4, respectively) and the NMR/X-ray structure of zf1-4 with the 17 bp DNA duplex (colors dark blue, dark green, dark maroon and brown for fingers 1–4, respectively). The coding and non-coding strands of the DNA are shown in gold and orange, respectively, except for the 5′ end of the non-coding strand of the X-ray structure, which is shown in red.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 372, 1227-1245) copyright 2007.

Figures were selected by the author.