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Title
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Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity.
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Authors
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D.S.Wuttke,
M.P.Foster,
D.A.Case,
J.M.Gottesfeld,
P.E.Wright.
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Ref.
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J Mol Biol, 1997,
273,
183-206.
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PubMed id
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Abstract
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The high resolution solution structure of a protein containing the three
amino-terminal zinc fingers of Xenopus laevis transcription factor IIIA (TFIIIA)
bound to its cognate DNA duplex was determined by nuclear magnetic resonance
spectroscopy. The protein, which is designated zf1-3, binds with all three
fingers in the DNA major groove, with a number of amino acids making
base-specific contacts. The DNA structure is close to B-form. Although the mode
of interaction of zf1-3 with DNA is similar to that of zif268 and other
structurally characterized zinc finger complexes, the TFIIIA complex exhibits
several novel features. Each zinc finger contacts four to five base-pairs and
the repertoire of known base contact residues is extended to include a
tryptophan at position +2 of the helix (finger 1) and arginine at position +10
(finger 3). Sequence-specific base contacts are made over virtually the entire
length of the finger 3 helix. Lysine and histidine side-chains involved in base
recognition are dynamically disordered in the solution structure; in the case of
lysine, in particular, this could significantly decrease the entropic cost of
DNA binding. The TGEKP(N) linker sequences, which are highly flexible in the
unbound protein, adopt ordered conformations on DNA binding. The linkers appear
to play an active structural role in stabilization of the protein-DNA complex.
Substantial protein-protein contact surfaces are formed between adjacent
fingers. As a consequence of these protein-protein interactions, the orientation
of finger 1 in the major groove differs from that of the other fingers.
Contributions to high affinity binding by zf1-3 come from both direct
protein-DNA contacts and from indirect protein-protein interactions associated
with structural organization of the linkers and formation of well-packed
interfaces between adjacent zinc fingers in the DNA complex. The structures
provide a molecular level explanation for the large body of footprinting and
mutagenesis data available for the TFIIIA-DNA complex.
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