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PDBsum entry 3gyh
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DNA binding protein/DNA
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PDB id
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3gyh
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Contents |
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* Residue conservation analysis
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Nature
459:808-813
(2009)
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PubMed id:
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Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
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J.L.Tubbs,
V.Latypov,
S.Kanugula,
A.Butt,
M.Melikishvili,
R.Kraehenbuehl,
O.Fleck,
A.Marriott,
A.J.Watson,
B.Verbeek,
G.McGown,
M.Thorncroft,
M.F.Santibanez-Koref,
C.Millington,
A.S.Arvai,
M.D.Kroeger,
L.A.Peterson,
D.M.Williams,
M.G.Fried,
G.P.Margison,
A.E.Pegg,
J.A.Tainer.
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ABSTRACT
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Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer
chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and
paradoxically protect cells from the biological effects of DNA alkylation
damage, despite lacking the reactive cysteine and alkyltransferase activity of
AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with
damaged DNA containing the endogenous lesion O(6)-methylguanine or
cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results
reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and
binding pocket size compared to AGT. Our analysis of lesion-binding site
conservation identifies new ATLs in sea anemone and ancestral archaea,
indicating that ATL interactions are ancestral to present-day repair pathways in
all domains of life. Genetic connections to mammalian XPG (also known as ERCC5)
and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions
with Escherichia coli UvrA and UvrC combined with structural results reveal that
ATLs sculpt alkylated DNA to create a genetic and structural intersection of
base damage processing with nucleotide excision repair.
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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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C.Yi,
B.Chen,
B.Qi,
W.Zhang,
G.Jia,
L.Zhang,
C.J.Li,
A.R.Dinner,
C.G.Yang,
and
C.He
(2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
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Nat Struct Mol Biol,
19,
671-676.
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PDB codes:
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G.M.Lingaraju,
C.A.Davis,
J.W.Setser,
L.D.Samson,
and
C.L.Drennan
(2011).
Structural basis for the inhibition of human alkyladenine DNA glycosylase (AAG) by 3,N4-ethenocytosine-containing DNA.
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J Biol Chem,
286,
13205-13213.
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PDB code:
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K.Wagner,
G.F.Moolenaar,
and
N.Goosen
(2011).
Role of the insertion domain and the zinc-finger motif of Escherichia coli UvrA in damage recognition and ATP hydrolysis.
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DNA Repair (Amst),
10,
483-496.
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T.Onodera,
K.Morino,
S.Tokishita,
R.Morita,
R.Masui,
S.Kuramitsu,
and
T.Ohta
(2011).
Role of alkyltransferase-like (ATL) protein in repair of methylated DNA lesions in Thermus thermophilus.
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Mutagenesis,
26,
303-308.
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E.H.Rubinson,
A.S.Gowda,
T.E.Spratt,
B.Gold,
and
B.F.Eichman
(2010).
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
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Nature,
468,
406-411.
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PDB codes:
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F.Liang,
and
B.P.Cho
(2010).
Enthalpy-entropy contribution to carcinogen-induced DNA conformational heterogeneity.
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Biochemistry,
49,
259-266.
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G.Lenglet,
and
M.H.David-Cordonnier
(2010).
DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences.
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J Nucleic Acids,
2010,
0.
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G.Mazon,
G.Philippin,
J.Cadet,
D.Gasparutto,
M.Modesti,
and
R.P.Fuchs
(2010).
Alkyltransferase-like protein (eATL) prevents mismatch repair-mediated toxicity induced by O6-alkylguanine adducts in Escherichia coli.
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Proc Natl Acad Sci U S A,
107,
18050-18055.
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H.Hashimoto,
P.M.Vertino,
and
X.Cheng
(2010).
Molecular coupling of DNA methylation and histone methylation.
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Epigenomics,
2,
657-669.
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J.L.Tubbs,
and
J.A.Tainer
(2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
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Cell Mol Life Sci,
67,
3749-3762.
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K.Fukui
(2010).
DNA mismatch repair in eukaryotes and bacteria.
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J Nucleic Acids,
2010,
0.
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R.Morita,
S.Nakane,
A.Shimada,
M.Inoue,
H.Iino,
T.Wakamatsu,
K.Fukui,
N.Nakagawa,
R.Masui,
and
S.Kuramitsu
(2010).
Molecular mechanisms of the whole DNA repair system: a comparison of bacterial and eukaryotic systems.
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J Nucleic Acids,
2010,
179594.
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R.P.Rambo,
and
J.A.Tainer
(2010).
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering.
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Curr Opin Struct Biol,
20,
128-137.
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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
