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PDBsum entry 2oqq
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Transcription
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PDB id
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2oqq
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References listed in PDB file
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Key reference
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Title
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Structural basis for the conformational integrity of the arabidopsis thaliana hy5 leucine zipper homodimer.
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Authors
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M.K.Yoon,
H.M.Kim,
G.Choi,
J.O.Lee,
B.S.Choi.
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Ref.
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J Biol Chem, 2007,
282,
12989-13002.
[DOI no: ]
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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
perfect match.
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Abstract
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The leucine zipper (LZ) domain of the HY5 transcription factor from Arabidopsis
thaliana has unique primary structural properties, including major occupation by
the Leu residues as well as two buried polar residues in the a positions and a
localized distribution of charged and polar residues in the first three heptad
repeats. In this study, we solved the crystal structure of the HY5 LZ domain and
show that the peculiarities in the primary sequence yield unusual structural
characteristics. For example, the HY5 LZ domain exhibits a bipartite charge
distribution characterized by a highly negative electrostatic surface potential
in its N-terminal half and a nearly neutral potential in its C-terminal half.
The LZ N-terminal region also contains two consecutive putative trigger sites
for dimerization of the coiled coils. In addition, two buried asparagines at a
positions 19 and 33 in the HY5 LZ domain display distinct modes of polar
interaction. Whereas Asn(19) shows a conformational flip-flop, Asn(33) is
engaged in a permanent hydrogen bond network. CD spectropolarimetry and
analytical ultracentrifugation experiments performed with versions of the HY5 LZ
domain containing mutations in the a positions yielded further evidence that
position a amino acid residues are crucial for achieving an oligomeric state and
maintaining stability. However, a low correlation between position a amino acid
preference, core packing geometry, and rotamer conformations suggests that the
oligomeric state of the LZ domain is not governed entirely by known structural
properties. Taken together, our results suggest structural factors conferring
conformational integrity of the HY5 LZ homodimer that are more complicated than
proposed previously.
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Figure 2.
FIGURE 2. Electrostatic interactions of the HY5 LZ
homodimer. A, helical wheel diagrams of the HY5 LZ homodimer.
The view is from the N terminus. Heptad positions are labeled
a-g. Solid and dashed gray lines indicate electrostatic
attractions between oppositely charged residues and hydrogen
bonds, respectively. Boxed amino acid residues are within the
putative trigger sites. The intrahelical hydrogen bond between
Leu^8 and Glu^9 in strand B was omitted for simplicity. B, front
(upper) and back (lower) views of electrostatic surface
potential representations of the HY5 LZ dimer. All positively
charged residues and some negatively charged residues that
interact with positive charges are labeled. Surface potentials
were calculated using GRASP (59).
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Figure 5.
FIGURE 5. Buried polar interactions of position a
asparagine residues in the HY5 LZ domain. A, the electron
densities (2F[o] - F[c]) contoured at 1.5  of Asn^19 (left) and
Asn^33 (right) from each helix strand are shown. Hydrogen bonds
formed between the side chains of asparagines from each monomer
are indicated by dashed green lines. B, shown is the extensive
hydrogen bond network of Asn^33 in the HY5 LZ domain.
Interstrand and non-helical intrastrand hydrogen bonds are
formed in and around Asn^33. Hydrogen bonds are indicated by
dashed green lines. Distances are expressed in angstroms. Ribbon
diagrams of the residues from strands A and B are shown in
orange and purple, respectively. C, the hexad structure of
Asn^33, which consists of
Glu^32-Asn^33-Arg^37/Glu^32'-Asn^33'-Arg^37' (upper), is
contrasted with the corresponding regions that contain
Lys^18-Asn^19-Glu^23/Lys^18'-Asn^19'-Glu^23' (lower). The hexad
structure of Asn^33 is tightly packed, whereas that of Asn^19 is
loosely packed. Polar, negatively charged, and positively
charged residues are colored yellow, red, and blue,
respectively. The figure was prepared with the program
Swiss-PdbViewer (39).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
12989-13002)
copyright 2007.
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