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PDBsum entry 2fdc
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DNA binding protein/DNA
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PDB id
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2fdc
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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 DNA recognition and processing by uvrb.
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Authors
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J.J.Truglio,
E.Karakas,
B.Rhau,
H.Wang,
M.J.Dellavecchia,
B.Van houten,
C.Kisker.
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Ref.
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Nat Struct Mol Biol, 2006,
13,
360-364.
[DOI no: ]
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PubMed id
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Abstract
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DNA-damage recognition in the nucleotide excision repair (NER) cascade is a
complex process, operating on a wide variety of damages. UvrB is the central
component in prokaryotic NER, directly involved in DNA-damage recognition and
guiding the DNA through repair synthesis. We report the first structure of a
UvrB-double-stranded DNA complex, providing insights into the mechanism by which
UvrB binds DNA, leading to formation of the preincision complex. One DNA strand,
containing a 3' overhang, threads behind a beta-hairpin motif of UvrB,
indicating that this motif inserts between the strands of the double helix,
thereby locking down either the damaged or undamaged strand. The nucleotide
directly behind the beta-hairpin is flipped out and inserted into a small,
highly conserved pocket in UvrB.
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Figure 1.
Figure 1. The UvrB–DNA complex and selected electron density.
(a) Surface of UvrB is color-coded by domain (yellow, 1a;
green, 1b; blue, 2; red, 3; cyan, the  -hairpin
of UvrB; magenta, the newly formed -sheet
after DNA binding). DNA is illustrated by spokes and letters,
color-coded by nucleotide type. The letter representation of the
DNA is in a similar orientation to the DNA in the structure.
Black letters, disordered nucleotides; F, fluorescein-adducted
thymine. The fluorescein-dT, although partially ordered (Fig.
1b), has been omitted from the figure for clarity. (b) 2F[o] -
F[c] electron density map contoured at 1.0  covering
the DNA. Gray, carbons of unmodified nucleotides; green, carbons
of partially ordered fluorescein; magenta, electron density for
the fluorescein. Nucleotides are labeled consecutively from 5'
to 3', omitting numbers of disordered residues. (c) UvrB–DNA
model showing how the inner strand of the DNA (red) travels
between the -hairpin
(cyan) and domain 1b and the outer strand (green) travels around
the outside of the -hairpin.
(d) Superposition of DNA-bound and apo UvrB. -hairpin
regions of the DNA-bound (cyan and blue) and apo UvrB (PDB entry
1D9X; yellow and gold) are superimposed. Select residues are
shown with color-coded labeling. Dark gray spokes represent the
bound DNA and the surface of the remainder of the UvrB–DNA
complex is shown in gray.
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Figure 2.
Figure 2. Interactions between UvrB and the DNA. (a) UvrB
bound to DNA. Gray surface, UvrB; cyan ribbon, -hairpin;
yellow, outer DNA strand; green, inner DNA strand. Selected
residues from UvrB are indicated. 3' and 5' ends of the DNA are
labeled in red. Nucleotides are numbered sequentially starting
from the 5' end and omitting numbers corresponding to
nucleotides in the loop region. (b,c) Views rotated  45°
(b) and 90°
(c) from a along the vertical axis.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
360-364)
copyright 2006.
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