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PDBsum entry 2prt
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Transcription/DNA
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PDB id
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2prt
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References listed in PDB file
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Key reference
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Title
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Structure of the wilms tumor suppressor protein zinc finger domain bound to DNA.
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Authors
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R.Stoll,
B.M.Lee,
E.W.Debler,
J.H.Laity,
I.A.Wilson,
H.J.Dyson,
P.E.Wright.
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Ref.
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J Mol Biol, 2007,
372,
1227-1245.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2007,
372,
1227-1245)
copyright 2007.
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