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PDBsum entry 1ahd
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DNA binding protein/DNA
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PDB id
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1ahd
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Determination of the nuclear magnetic resonance solution structure of an antennapedia homeodomain-Dna complex.
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Authors
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M.Billeter,
Y.Q.Qian,
G.Otting,
M.Müller,
W.Gehring,
K.Wüthrich.
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Ref.
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J Mol Biol, 1993,
234,
1084-1093.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
85%.
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Abstract
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The nuclear magnetic resonance (NMR) solution structure of a complex formed by
the mutant Antennapedia homeodomain with Cys39 replaced by Ser, Antp(C39S), and
a 14 base-pair DNA duplex containing the BS2 operator sequence was determined
using uniform 13C and 15N-labeling of the protein. Two-dimensional nuclear
Overhauser enhancement spectroscopy ([1H,1H]NOESY) with 15N(omega 2)-half-filter
and 13C(omega 1, omega 2)-double-half-filter, and three-dimensional
heteronuclear-correlated [1H,1H]NOESY yielded a total of 855 intramolecular NOE
upper distance constraints in the homeodomain, 151 upper distance constraints
within the DNA duplex, and 39 intermolecular protein-DNA upper distance
constraints. These data were used as the input for the structure calculation
with simulated annealing followed by molecular dynamics in a water bath and
energy refinement. A group of 16 conformers was thus generated which represent
the solution structure of the Antp(C39S) homeodomain-DNA complex. The new
structure determination confirms the salient features reported previously from a
preliminary investigation of the same complex, in particular the location of the
recognition helix in the major groove with the turn of the helix-turn-helix
motif outside the contact area with the DNA, and the N-terminal arm of the
homeodomain contacting the minor groove of the DNA. In addition, distinct amino
acid side-chain-DNA contacts could be identified, and evidence was found that
the invariant residue Asn51 (and possibly also Gln50) is in a slow dynamic
equilibrium between two or several different DNA contact sites. The molecular
dynamics calculations in a water bath yielded structures with hydration water
molecules in the protein-DNA interface, which coincides with direct NMR
observations of hydration waters. In the Appendix the experimental data obtained
with the Antp(C39S) homeodomain-DNA complex and the techniques used for the
structure calculation are evaluated using a simulated input data set derived
from the X-ray crystal structure of a DNA complex with a homologous homeodomain.
This study indicates that a nearly complete set of NOE upper distance
constraints for the Antp(C39S) homeodomain and the protein-DNA interface was
presently obtained. It further shows that the structure calculation used here
yields a precise reproduction of the crystal structure from the simulated input
data, and also results in hydration of the protein-DNA interface in the
recalculated complex.
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Secondary reference #1
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Title
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Nuclear magnetic resonance spectroscopy of a DNA complex with the uniformly 13c-Labeled antennapedia homeodomain and structure determination of the DNA-Bound homeodomain.
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Authors
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Y.Q.Qian,
G.Otting,
M.Billeter,
M.Müller,
W.Gehring,
K.Wüthrich.
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Ref.
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J Mol Biol, 1993,
234,
1070-1083.
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
89%.
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Secondary reference #2
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Title
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Determination of the three-Dimensional structure of the antennapedia homeodomain from drosophila in solution by 1h nuclear magnetic resonance spectroscopy.
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Authors
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M.Billeter,
Y.Qian,
G.Otting,
M.Müller,
W.J.Gehring,
K.Wüthrich.
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Ref.
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J Mol Biol, 1990,
214,
183-197.
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PubMed id
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Secondary reference #3
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Title
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Protein--Dna contacts in the structure of a homeodomain--Dna complex determined by nuclear magnetic resonance spectroscopy in solution.
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Authors
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G.Otting,
Y.Q.Qian,
M.Billeter,
M.Müller,
M.Affolter,
W.J.Gehring,
K.Wüthrich.
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Ref.
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Embo J, 1990,
9,
3085-3092.
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PubMed id
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Secondary reference #4
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Title
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The structure of the antennapedia homeodomain determined by nmr spectroscopy in solution: comparison with prokaryotic repressors.
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Authors
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Y.Q.Qian,
M.Billeter,
G.Otting,
M.Müller,
W.J.Gehring,
K.Wüthrich.
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Ref.
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Cell, 1989,
59,
573-580.
[DOI no: ]
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PubMed id
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