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PDBsum entry 1b4b
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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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Structure of the arginine repressor from bacillus stearothermophilus.
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Authors
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J.Ni,
V.Sakanyan,
D.Charlier,
N.Glansdorff,
G.D.Van duyne.
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Ref.
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Nat Struct Biol, 1999,
6,
427-432.
[DOI no: ]
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PubMed id
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Abstract
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The arginine repressor (ArgR) is a hexameric DNA-binding protein that plays a
multifunctional role in the bacterial cell. Here, we present the 2.5 A structure
of apo-ArgR from Bacillus stearothermophilus and the 2.2 A structure of the
hexameric ArgR oligomerization domain with bound arginine. This first view of
intact ArgR reveals an approximately 32-symmetric hexamer of identical subunits,
with six DNA-binding domains surrounding a central oligomeric core. The
difference in quaternary organization of subunits in the arginine-bound and apo
forms provides a possible explanation for poor operator binding by apo-ArgR and
for high affinity binding in the presence of arginine.
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Figure 2.
Figure 2. a, Ribbon drawing of the ArgRBst-C hexamer, viewed
along the local threefold symmetry axis. Bound arginine
molecules are drawn as ball-and-stick models. b, Ribbon drawing
of the ArgRBst-C hexamer with bound arginines, viewed along a
dyad symmetry axis, perpendicular to the view in (a). c,
Superposition of C  atoms
for the apo-ArgRBst core hexamer (pink and green trimers) and
the ArgRBst-C core hexamer (blue). Only the bottom (pink) trimer
of the ArgRBst core hexamer was used to perform the
superposition (r.m.s. difference of 1 Å). The view is the
same as in (a). d, Superposition as in (c), except viewed along
a dyad axis, as in ( b). Figs 2, 3a,b, and 4 were prepared using
RIBBONS^33.
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Figure 4.
Figure 4. a, Model of the apo-ArgRBst−DNA interaction. The
apoArgRBst hexamer is shown superimposed on the arginine-bound
ArgRBst−C hexamer as in Fig. 2c, but with the bottom trimers
removed for clarity. DNA-binding domains are labeled a-f at the
3
helices. The bent DNA duplex from the CAP/DNA complex^23 was
extended in both directions to give a total length of 38 base
pairs, docked with the apo-ArgRBst hexamer, then undocked for
clarity. Arrows indicate clashes between the 3
helices and the phosphate backbone of the DNA duplex. b, Model
of the arginine-bound ArgRBst−DNA interaction. The top (green)
trimer in ArgRBst was independently rotated (by ~15°) onto
the ArgRBst-C core trimer to approximate the quaternary
structure of ArgRBst in the arginine-bound state. Arrows
indicate 3-major
groove contacts when docked with the hexamer in the orientation
shown. c, Schematic representation of ArgR DNA operators. E.
coli operators contain 18 base pair 'Arg boxes' separated by a
2−3 base pair spacer^21, ^22. Arrows indicate 9 base pair
half-sites that are arranged as inverted repeats within the E.
coli consensus Arg box sequence. The B. subtilis and B.
stearothermophilus operator sequences show only limited homology
to the E. coli operators, but similar nuclease and chemical
protection patterns and the ability of B. subtilis AhrC to
complement ArgR functions in E. coli indicate that the
repressor−operator interactions are closely related^3, ^8.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(1999,
6,
427-432)
copyright 1999.
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Secondary reference #1
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Title
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Author
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J.Ni.
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Ref.
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the crystal structure of ...
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