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PDBsum entry 1xrx
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Replication inhibitor
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PDB id
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1xrx
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a seqa-N filament: implications for DNA replication and chromosome organization.
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Authors
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A.Guarné,
T.Brendler,
Q.Zhao,
R.Ghirlando,
S.Austin,
W.Yang.
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Ref.
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EMBO J, 2005,
24,
1502-1511.
[DOI no: ]
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PubMed id
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Abstract
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Escherichia coli SeqA binds clusters of transiently hemimethylated GATC
sequences and sequesters the origin of replication, oriC, from methylation and
premature reinitiation. Besides oriC, SeqA binds and organizes newly synthesized
DNA at replication forks. Binding to multiple GATC sites is crucial for the
formation of stable SeqA-DNA complexes. Here we report the crystal structure of
the oligomerization domain of SeqA (SeqA-N). The structural unit of SeqA-N is a
dimer, which oligomerizes to form a filament. Mutations that disrupt filament
formation lead to asynchronous DNA replication, but the resulting SeqA dimer can
still bind two GATC sites separated from 5 to 34 base pairs. Truncation of the
linker between the oligomerization and DNA-binding domains restricts SeqA to
bind two GATC sites separated by one or two full turns. We propose a model of a
SeqA filament interacting with multiple GATC sites that accounts for both origin
sequestration and chromosome organization.
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Figure 1.
Figure 1 Oligomerization of the SeqA -N dimer. (A) Ribbon
diagram of a single SeqA -N subunit. (B) A SeqA -N dimer. The
two subunits are shown as yellow and green ribbon diagrams. (C)
The asymmetric unit contains two SeqA -N dimers related by a
noncrystallographic dyad axis and a 4[3] screw axis. The two
SeqA -N dimers colored yellow -green and blue -red,
respectively, are shown in a ribbons diagram (left) and
molecular surface representation (right). (D) Two views of the
SeqA -N filament. The black bar indicates a complete helical
turn consisting of four dimers. The 4[3] axis and the
noncrystallographic (gray arrows) and crystallographic (gray
ovals) dyad axes are indicated. (E) Crystal packing of the SeqA
filaments shown as a ribbon diagram. Filaments pack according to
the crystallographic 3[1] axis. The central filament is shown
with the SeqA monomers colored yellow and green. The top and
bottom filaments are shown in light and dark gray, respectively.
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Figure 5.
Figure 5 A model of the interactions between a SeqA filament and
DNA. (A) A SeqA -N dimer and a pair of crystallographic SeqA -C
-DNA complexes are placed to share a common dyad axis. The
protein is shown as ribbon diagrams in dark (SeqA -N) and light
(SeqA -C) blue and the DNA depicted as stick models. (B) The
full-length SeqA dimer -DNA model is allowed to multimerize
according to the 4[3] screw axis of the SeqA -N filament. The
four-fold screw axis is perpendicular to the plane. Each SeqA -N
dimer and the SeqA -C pair bound to it are shown in dark and
light shades of a distinct color. Space between the N- and
C-terminal domains accounts for the flexible linker and avoids
contacts or clashes between neighboring SeqA -C molecules
related by the 4[3] screw axis. An orthogonal view placing the
SeqA -DNA superhelix in plane is shown on the right panel. No
artificial coordinates are introduced, and DNAs are left to be
discontinuous between adjacent SeqA dimers. Scale bars represent
100 Å.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2005,
24,
1502-1511)
copyright 2005.
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