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PDBsum entry 1arf
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Transcription regulation
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PDB id
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1arf
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DOI no:
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Protein Sci
2:951-965
(1993)
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PubMed id:
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Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
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R.C.Hoffman,
S.J.Horvath,
R.E.Klevit.
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ABSTRACT
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Studies of Cys2-His2 zinc finger domains have revealed that the structures of
individual finger domains in solution determined by NMR spectroscopy are
strikingly similar to the structure of fingers bound to DNA determined by X-ray
diffraction. Therefore, detailed structural analyses of single finger domains
that contain amino acid substitutions known to affect DNA binding in the whole
protein can yield information concerning the structural ramifications of such
mutations. We have used this approach to study two mutants in the N-terminal
finger domain of ADR1, a yeast transcription factor that contains two Cys2-His2
zinc finger sequences spanning residues 102-159. Two point mutants at position
118 in the N-terminal zinc finger (ADR1b: 102-130) that adversely affect the
DNA-binding activity of ADR1 have previously been identified: H118A and H118Y.
The structures of wild-type ADR1b and the two mutant zinc finger domains were
determined using two-dimensional nuclear magnetic resonance spectroscopy and
distance geometry and were refined using a complete relaxation matrix method
approach (REPENT) to improve agreement between the models and the nuclear
Overhauser effect spectroscopy data from which they were generated. The
molecular architecture of the refined wild-type ADR1b domain is presented in
detail. Comparisons of wild-type ADR1b and the two mutants revealed that neither
mutation causes a significant structural perturbation. The structures indicate
that the DNA binding properties of the His 118 mutants are dependent on the
identity of the side chain at position 118, which has been postulated to make a
direct DNA contact in the wild-type ADR1 protein. The results suggest that the
identity of the side chain at the middle DNA contact position in Cys2-His2 zinc
fingers may be changed with impunity regarding the domain structure and can
affect the affinity of the protein-DNA interaction.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.J.Freedman,
Z.Y.Sun,
A.L.Kung,
D.S.France,
G.Wagner,
and
M.J.Eck
(2003).
Structural basis for negative regulation of hypoxia-inducible factor-1alpha by CITED2.
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Nat Struct Biol,
10,
504-512.
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PDB code:
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M.Schmiedeskamp,
P.Rajagopal,
and
R.E.Klevit
(1997).
NMR chemical shift perturbation mapping of DNA binding by a zinc-finger domain from the yeast transcription factor ADR1.
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Protein Sci,
6,
1835-1848.
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M.Schmiedeskamp,
and
R.E.Klevit
(1997).
Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein.
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Biochemistry,
36,
14003-14011.
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R.N.Dutnall,
D.Neuhaus,
and
D.Rhodes
(1996).
The solution structure of the first zinc finger domain of SWI5: a novel structural extension to a common fold.
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Structure,
4,
599-611.
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PDB code:
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T.N.Jaishree,
V.Ramakrishnan,
and
S.W.White
(1996).
Solution structure of prokaryotic ribosomal protein S17 by high-resolution NMR spectroscopy.
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Biochemistry,
35,
2845-2853.
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V.V.Svetlov,
and
T.G.Cooper
(1995).
Review: compilation and characteristics of dedicated transcription factors in Saccharomyces cerevisiae.
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Yeast,
11,
1439-1484.
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B.E.Bernstein,
R.C.Hoffman,
and
R.E.Klevit
(1994).
Sequence-specific DNA recognition by Cys2, His2 zinc fingers.
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Ann N Y Acad Sci,
726,
92.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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Links
