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PDBsum entry 1zq3
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Transcription/DNA
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PDB id
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1zq3
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References listed in PDB file
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Key reference
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Title
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The solution structure of the native k50 bicoid homeodomain bound to the consensus taatcc DNA-Binding site.
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Authors
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J.M.Baird-Titus,
K.Clark-Baldwin,
V.Dave,
C.A.Caperelli,
J.Ma,
M.Rance.
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Ref.
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J Mol Biol, 2006,
356,
1137-1151.
[DOI no: ]
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PubMed id
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Abstract
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The solution structure of the homeodomain of the Drosophila morphogenic protein
Bicoid (Bcd) complexed with a TAATCC DNA site is described. Bicoid is the only
known protein that uses a homeodomain to regulate translation, as well as
transcription, by binding to both RNA and DNA during early Drosophila
development; in addition, the Bcd homeodomain can recognize an array of
different DNA sites. The dual functionality and broad recognition capabilities
signify that the Bcd homeodomain may possess unique structural/dynamic
properties. Bicoid is the founding member of the K50 class of homeodomain
proteins, containing a lysine residue at the critical 50th position (K50) of the
homeodomain sequence, a residue required for DNA and RNA recognition; Bcd also
has an arginine residue at the 54th position (R54), which is essential for RNA
recognition. Bcd is the only known homeodomain with the K50/R54 combination of
residues. The Bcd structure indicates that this homeodomain conforms to the
conserved topology of the homeodomain motif, but exhibits a significant
variation from other homeodomain structures at the end of helix 1. A key result
is the observation that the side-chains of the DNA-contacting residues K50, N51
and R54 all show strong signs of flexibility in the protein-DNA interface. This
finding is supportive of the adaptive-recognition theory of protein-DNA
interactions.
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Figure 2.
Figure 2. Description of the DNA site used for this study
and its structure. (a) Schematic and numbering scheme of the
13mer DNA duplex used for this study. The 5' ends of each strand
are base numbers 1 and 14. (b) Three structures of the DNA seen
during various stages of the structure calculation. The original
B-DNA model created using the program NUCGEN (red), the mean
structure after the initial docking calculation (green), and the
mean structure after the final energy minimization in the
absence of all constraints (blue) are superimposed.
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Figure 4.
Figure 4. Superimposed C^a atom ribbon diagrams of 16
homeodomains (see the text for a list). The region of high local
RMSD difference between the Bicoid homeodomain (red) and the
rest (grey) is labeled with a red arrow. The Bicoid homeodomain
contains glycine in position 23, which results in reduced
hydrogen-bonding ability to nearby residues and an alteration of
the homeodomain structure when compared to the 15 other
homeodomain structures. The functional significance of this
difference is unknown.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
356,
1137-1151)
copyright 2006.
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