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PDBsum entry 1d9z
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Gene regulation
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PDB id
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1d9z
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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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Crystal structure of uvrb, A DNA helicase adapted for nucleotide excision repair.
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Authors
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K.Theis,
P.J.Chen,
M.Skorvaga,
B.Van houten,
C.Kisker.
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Ref.
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EMBO J, 1999,
18,
6899-6907.
[DOI no: ]
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PubMed id
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Abstract
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Nucleotide excision repair (NER) is a highly conserved DNA repair mechanism. NER
systems recognize the damaged DNA strand, cleave it on both sides of the lesion,
remove and newly synthesize the fragment. UvrB is a central component of the
bacterial NER system participating in damage recognition, strand excision and
repair synthesis. We have solved the crystal structure of UvrB in the apo and
the ATP-bound forms. UvrB contains two domains related in structure to
helicases, and two additional domains unique to repair proteins. The structure
contains all elements of an intact helicase, and is evidence that UvrB utilizes
ATP hydrolysis to move along the DNA to probe for damage. The location of
conserved residues and structural comparisons allow us to predict the path of
the DNA and suggest that the tight pre-incision complex of UvrB and the damaged
DNA is formed by insertion of a flexible beta-hairpin between the two DNA
strands.
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Figure 2.
Figure 2 The ATP binding site. Residues in the vicinity of the
ATP are shown in an all-bonds representation. The ATP molecule
is shown as a ball-and-stick model and the Mg2+ ion is indicated
by a sphere; hydrogen bonds are shown as dotted lines.
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Figure 3.
Figure 3 Conserved residues and electrostatic potential on the
surface of UvrB. For a better view into the ATP binding site,
domain 3 has been rotated by 120° away from the remainder of
UvrB to show the interface between domains 1a and 3. The ATP
molecule has been duplicated in the figure, shown in its
orientation with respect to domains 1a and 3. Residues 96 -98
and 109 -113 were omitted from the surface calculation and are
shown as a cyan backbone worm for a better view into the cleft
between domains 1a and 1b. (A) Side chains on the surface of
UvrB that are conserved throughout 16 UvrB sequences are colored
according to their location in helicase motifs I-VI. Magenta,
motifs I and IV; green, motifs II and V; blue, motifs III and
VI; yellow, conserved residues not belonging to any helicase
motif. (B) Electrostatic potential calculated separately for
domain 3 and for the remainder of the molecule including the
bound ATP, at an ionic strength of 0.1 M contoured at  10
k[B]T (k[B] is the Boltzmann constant and T the absolute
temperature). Blue, positively charged; red, negatively charged.
Figures 3 and 5 were made using GRASP (Nicholls et al., 1991).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(1999,
18,
6899-6907)
copyright 1999.
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Secondary reference #1
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Title
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Strand opening by the uvra(2)b complex allows dynamic recognition of DNA damage.
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Authors
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Y.Zou,
B.Van houten.
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Ref.
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EMBO J, 1999,
18,
4889-4901.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6 Binding of UvrA and UvrB proteins to the BPDE-DNA
bubble substrates. The substrates (4 nM) with different sizes of
bubble structure were incubated with UvrA (10 nM) and UvrB (100
nM) at 37°C for 15 min in the UvrABC buffer with 1 mM ATP. After
the incubation, the samples were loaded immediately onto a 4%
native polyacrylamide gel for electrophoresis. ND, non-damaged
DNA without bubble; UvrAB- and UvrB -DNA, the protein -DNA
complexes formed with UvrAB and UvrB, respectively.
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Figure 7.
Figure 7 Schematic representation of the pre-incision complex
formed between UvrBC and damaged DNA. With the early
participation of UvrA, the damaged DNA is unwound around the
adduct, and an open DNA structure forms with UvrBC proteins,
which is characterized by 2 unpaired bases 5' and 3 unpaired
bases 3' to the adduct. The 3' and 5' double-stranded nuclease
activities of UvrBC incise the damage 1 base 3' and 6 bases 5'
to the open structure, respectively. In addition, we propose a
direct interaction between the UvrBC and the adducted base. The
yellow, violet, green and blue colored sticks in the DNA strands
represent the bases cytosine, thymine, adenine and guanine,
respectively. The red stick represents the adducted guanine.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by Macmillan Publishers Ltd
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