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PDBsum entry 1ba5
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DNA-binding domain
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PDB id
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1ba5
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References listed in PDB file
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Key reference
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Title
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Solution structure of the DNA-Binding domain of human telomeric protein, Htrf1.
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Authors
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T.Nishikawa,
A.Nagadoi,
S.Yoshimura,
S.Aimoto,
Y.Nishimura.
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Ref.
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Structure, 1998,
6,
1057-1065.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Mammalian telomeres consist of long tandem arrays of the
double-stranded TTAGGG sequence motif packaged by a telomere repeat binding
factor, TRF1. The DNA-binding domain of TRF1 shows sequence homology to each of
three tandem repeats of the DNA-binding domain of the transcriptional activator
c-Myb. The isolated c-Myb-like domain of human TRF1 (hTRF1) binds specifically
to telomeric DNA as a monomer, in a similar manner to that of homeodomains. So
far, the only three-dimensional structure of a telomeric protein to be
determined is that of a yeast telomeric protein, Rap 1p. The DNA-binding domain
of Rap 1p contains two subdomains that are structurally closely related to c-Myb
repeats. We set out to determine the solution structure of the DNA-binding
domain of hTRF1 in order to establish its mode of DNA binding. RESULTS: The
solution structure of the DNA-binding domain of hTRF1 has been determined and
shown to comprise three helices. The architecture of the three helices is very
similar to that of each Rap 1p subdomain and also to that of each c-Myb repeat.
The second and third helix form a helix-turn-helix (HTH) variant. The length of
the third helix of hTRF1 is similar to that of the second subdomain of Rap 1p.
CONCLUSIONS: The hTRF1 DNA-binding domain is likely to bind to DNA in a similar
manner to that of the second subdomain of Rap 1p. On the basis of the Rap 1p-DNA
complex, a model of the hTRF1 DNA-binding domain in complex with human telomeric
DNA was constructed. In addition to DNA recognition by the HTH variant, a
flexible N-terminal arm of hTRF1 is likely to interact with DNA.
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Figure 3.
Figure 3. Stereoviews of the hTRF1 DNA-binding domain
structures. Backbone atoms and sidechain atoms are shown in
yellow and red, respectively; the N and C termini are marked.
(a) The best-fit superposition of the 18 structures; three
tryptophans and one phenylalanine residue form the hydrophobic
core. (b) The refined average structure again showing the amino
acids that form the hydrophobic core.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1998,
6,
1057-1065)
copyright 1998.
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