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* Residue conservation analysis
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DOI no:
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J Mol Biol
357:62-72
(2006)
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PubMed id:
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Structural insights into the cryptic DNA-dependent ATPase activity of UvrB.
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J.Eryilmaz,
S.Ceschini,
J.Ryan,
S.Geddes,
T.R.Waters,
T.E.Barrett.
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ABSTRACT
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The UvrABC pathway is a ubiquitously occurring mechanism targeted towards the
repair of bulky base damage. Key to this process is UvrB, a DNA-dependent
limited helicase that acts as a lesion recognition element whilst part of a
tracking complex involving UvrA, and as a DNA-binding platform required for the
presentation of damage to UvrC for subsequent processing. We have been able to
determine the structure of a ternary complex involving UvrB* (a C-terminal
truncation of full-length UvrB), a polythymine trinucleotide and ADP. This
structure has highlighted the roles of key conserved residues in DNA binding
distinct from those of the beta-hairpin, where most of the attention in previous
studies has been focussed. We are also the first to report the structural basis
underlying conformational re-modelling of the beta-hairpin that is absolutely
required for DNA binding and how this event results in an ATPase primed for
catalysis. Our data provide the first insights at the molecular level into the
transformation of UvrB into an active helicase.
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Selected figure(s)
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Figure 2.
Figure 2. (a) The 2F[o] -F[c] omit map contoured at 1s for
the trithymine oligonucleotide. (b) Protein-DNA interactions.
The trinucleotide binds at the entrance to a channel in the
interface between the b-hairpin loop and residues comprising
domains 1a and 1b. The majority of contacts involve hydrogen
bonds between the phosphate groups of the thymine nucleotides
(5'-T1 to T3-3') and residues Thr481 in domain 3, Lys67 in
domain 1a, Ser 91 at the N terminus of the b-hairpin loop and
Ser141 (also in domain 1a). The furanose sugar and base of T3
stack against the aryl moieties of Tyr146 and Tyr96,
respectively.
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Figure 6.
Figure 6. The relative positions of a modelled g-phosphate
group, DEAD/H box (yellow), Lys67 together with its near
environment (red) and tyrosine residues that form the base of
the b-hairpin (magenta). These elements are all favourably
juxtaposed for the transduction of signals between the ATP and
DNA-binding sites.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2006,
357,
62-72)
copyright 2006.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Pakotiprapha,
M.Samuels,
K.Shen,
J.H.Hu,
and
D.Jeruzalmi
(2012).
Structure and mechanism of the UvrA-UvrB DNA damage sensor.
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Nat Struct Mol Biol,
19,
291-298.
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PDB codes:
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L.Jia,
K.Kropachev,
S.Ding,
B.Van Houten,
N.E.Geacintov,
and
S.Broyde
(2009).
Exploring damage recognition models in prokaryotic nucleotide excision repair with a benzo[a]pyrene-derived lesion in UvrB.
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Biochemistry,
48,
8948-8957.
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N.T.Uyen,
S.Y.Park,
J.W.Choi,
H.J.Lee,
K.Nishi,
and
J.S.Kim
(2009).
The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity.
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Nucleic Acids Res,
37,
6960-6969.
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PDB code:
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D.L.Croteau,
M.J.DellaVecchia,
L.Perera,
and
B.Van Houten
(2008).
Cooperative damage recognition by UvrA and UvrB: identification of UvrA residues that mediate DNA binding.
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DNA Repair (Amst),
7,
392-404.
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D.Pakotiprapha,
Y.Inuzuka,
B.R.Bowman,
G.F.Moolenaar,
N.Goosen,
D.Jeruzalmi,
and
G.L.Verdine
(2008).
Crystal structure of Bacillus stearothermophilus UvrA provides insight into ATP-modulated dimerization, UvrB interaction, and DNA binding.
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Mol Cell,
29,
122-133.
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PDB code:
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J.M.Aramini,
S.Sharma,
Y.J.Huang,
G.V.Swapna,
C.K.Ho,
K.Shetty,
K.Cunningham,
L.C.Ma,
L.Zhao,
L.A.Owens,
M.Jiang,
R.Xiao,
J.Liu,
M.C.Baran,
T.B.Acton,
B.Rost,
and
G.T.Montelione
(2008).
Solution NMR structure of the SOS response protein YnzC from Bacillus subtilis.
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Proteins,
72,
526-530.
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PDB codes:
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M.J.DellaVecchia,
W.K.Merritt,
Y.Peng,
T.W.Kirby,
E.F.DeRose,
G.A.Mueller,
B.Van Houten,
and
R.E.London
(2007).
NMR analysis of [methyl-13C]methionine UvrB from Bacillus caldotenax reveals UvrB-domain 4 heterodimer formation in solution.
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J Mol Biol,
373,
282-295.
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H.Wang,
M.J.DellaVecchia,
M.Skorvaga,
D.L.Croteau,
D.A.Erie,
and
B.Van Houten
(2006).
UvrB domain 4, an autoinhibitory gate for regulation of DNA binding and ATPase activity.
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J Biol Chem,
281,
15227-15237.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
