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PDBsum entry 2gcc
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Transcription factor
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PDB id
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2gcc
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References listed in PDB file
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Key reference
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Title
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A novel mode of DNA recognition by a beta-Sheet revealed by the solution structure of the gcc-Box binding domain in complex with DNA.
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Authors
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M.D.Allen,
K.Yamasaki,
M.Ohme-Takagi,
M.Tateno,
M.Suzuki.
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Ref.
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Embo J, 1998,
17,
5484-5496.
[DOI no: ]
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PubMed id
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Abstract
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The 3D solution structure of the GCC-box binding domain of a protein from
Arabidopsis thaliana in complex with its target DNA fragment has been determined
by heteronuclear multidimensional NMR in combination with simulated annealing
and restrained molecular dynamic calculation. The domain consists of a
three-stranded anti-parallel beta-sheet and an alpha-helix packed approximately
parallel to the beta-sheet. Arginine and tryptophan residues in the beta-sheet
are identified to contact eight of the nine consecutive base pairs in the major
groove, and at the same time bind to the sugar phosphate backbones. The target
DNA bends slightly at the central CG step, thereby allowing the DNA to follow
the curvature of the beta-sheet.
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Figure 2.
Figure 2 Comparison of GBD with a zinc finger. (A) Superposition
of the backbones of 46 GBD structures, Lys145-Val206, in the
absence of the DNA refined by simulated annealing. Different
colors are used for indicating the secondary structural
elements. The N- and C-termini are labeled. (B) A diagrammatic
drawing of the final structure made by energy minimization of
the mean co-ordinates of the ensemble shown in (A), superimposed
on a presentation of electropolarization. Positive charges are
shown in blue and negative charges in red. The side that
recognizes DNA is indicated with an arrow. (C) The 3D structure
and electropolarization of the first zinc finger of SWI5
(Protein Data Bank code 1NCS) shown in the same way as in (B).
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Figure 5.
Figure 5 Contacts between GBD and the GCC-box. (A) A stereo
subfigure of part of the GBD -DNA complex structure. The
contacts are indicated by broken lines with different colors;
green for hydrogen bonds and yellow for ionic contacts.
Different colors are used for the coding (crimson) and
complementary (cyan) strands. (B) A diagrammatic representation
of the contacts identified after restrained molecular dynamic
calculation. The DNA is drawn by looking into the major groove.
Yellow circles represent the phosphate groups. The contacted
bases are highlighted in cyan. The same color code as in (A) is
used for typing the contacts and, in addition, brown for
hydrophobic contacts. The distance between Glu160 and C19 is
slightly larger than the standard hydrogen bonding distance
(shown by a broken line). The up -down transcription direction
is indicated. The coding and complementary strands are labeled.
Gd: guanidyl group. (C) A diagrammatic representation of the
NOEs observed between amino acid residues and the target DNA.
The bases with which the NOEs are observed are highlighted in
orange. (D) The three stranded  -sheet
of GBD. Residues are colored differently depending on the
function; base-contacting only (blue), backbone-binding only
(yellow) and having both functions (green). An ellipsoid is
drawn by connecting the green positions, which is divided into
two halves by the broken line that crosses Ala159. The CG step
is highlighted in cyan. The up -down transcription direction is
indicated. The coding and complementary strands are labeled. (E)
A two stranded -sheet
of the MetJ -Arc type. The figure was made using the
co-ordinates of the MetJ -DNA complex (Protein Data Base code
1CMA). The six amino acid positions used for base recognition by
the MetJ -Arc family are in blue. An ellipsoid is drawn
enclosing the blue residues. Compare the ellipsoid with the
larger ellipsoid shown in (D) for an appreciation of the
difference in size of the two interaction sites.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
Embo J
(1998,
17,
5484-5496)
copyright 1998.
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