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PDBsum entry 3gpu
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Contents |
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* Residue conservation analysis
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Enzyme class 1:
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E.C.3.2.2.23
- DNA-formamidopyrimidine glycosylase.
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Reaction:
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Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
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Enzyme class 2:
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E.C.4.2.99.18
- DNA-(apurinic or apyrimidinic site) lyase.
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Reaction:
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2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H+
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Note, where more than one E.C. class is given (as above), each may
correspond to a different protein domain or, in the case of polyprotein
precursors, to a different mature protein.
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Nature
462:762-766
(2009)
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PubMed id:
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Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
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Y.Qi,
M.C.Spong,
K.Nam,
A.Banerjee,
S.Jiralerspong,
M.Karplus,
G.L.Verdine.
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ABSTRACT
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How living systems detect the presence of genotoxic damage embedded in a
million-fold excess of undamaged DNA is an unresolved question in biology. Here
we have captured and structurally elucidated a base-excision DNA repair enzyme,
MutM, at the stage of initial encounter with a damaged nucleobase, 8-oxoguanine
(oxoG), nested within a DNA duplex. Three structures of intrahelical
oxoG-encounter complexes are compared with sequence-matched structures
containing a normal G base in place of an oxoG lesion. Although the protein-DNA
interfaces in the matched complexes differ by only two atoms-those that
distinguish oxoG from G-their pronounced structural differences indicate that
MutM can detect a lesion in DNA even at the earliest stages of encounter.
All-atom computer simulations show the pathway by which encounter of the enzyme
with the lesion causes extrusion from the DNA duplex, and they elucidate the
critical free energy difference between oxoG and G along the extrusion pathway.
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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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M.Firczuk,
M.Wojciechowski,
H.Czapinska,
and
M.Bochtler
(2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
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Nucleic Acids Res,
39,
744-754.
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PDB code:
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C.Yi,
G.Jia,
G.Hou,
Q.Dai,
W.Zhang,
G.Zheng,
X.Jian,
C.G.Yang,
Q.Cui,
and
C.He
(2010).
Iron-catalysed oxidation intermediates captured in a DNA repair dioxygenase.
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Nature,
468,
330-333.
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PDB codes:
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G.M.Li
(2010).
Novel molecular insights into the mechanism of GO removal by MutM.
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Cell Res,
20,
116-118.
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R.P.Rambo,
G.J.Williams,
and
J.A.Tainer
(2010).
Achieving fidelity in homologous recombination despite extreme complexity: informed decisions by molecular profiling.
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Mol Cell,
40,
347-348.
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Y.Qi,
M.C.Spong,
K.Nam,
M.Karplus,
and
G.L.Verdine
(2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
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J Biol Chem,
285,
1468-1478.
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PDB codes:
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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
