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PDBsum entry 2v4r
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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 and functional analysis of sulfolobus solfataricus y-Family DNA polymerase dpo4-Catalyzed bypass of the malondialdehyde-Deoxyguanosine adduct.
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Authors
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R.L.Eoff,
J.B.Stafford,
J.Szekely,
C.J.Rizzo,
M.Egli,
F.P.Guengerich,
L.J.Marnett.
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Ref.
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Biochemistry, 2009,
48,
7079-7088.
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PubMed id
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Abstract
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Oxidative stress can induce the formation of reactive electrophiles, such as DNA
peroxidation products, e.g., base propenals, and lipid peroxidation products,
e.g., malondialdehyde. Base propenals and malondialdehyde react with DNA to form
adducts, including
3-(2'-deoxy-beta-D-erythro-pentofuranosyl)pyrimido[1,2-alpha]purin-10(3H)-one
(M1dG). When paired opposite cytosine in duplex DNA at physiological pH, M1dG
undergoes ring opening to form N2-(3-oxo-1-propenyl)-dG (N2-OPdG). Previous work
has shown that M1dG is mutagenic in bacteria and mammalian cells and that its
mutagenicity in Escherichia coli is dependent on induction of the SOS response,
indicating a role for translesion DNA polymerases in the bypass of M1dG. To
probe the mechanism by which translesion polymerases bypass M1dG, kinetic and
structural studies were conducted with a model Y-family DNA polymerase, Dpo4
from Sulfolobus solfataricus. The level of steady-state incorporation of dNTPs
opposite M1dG was reduced 260-2900-fold and exhibited a preference for dATP
incorporation. Liquid chromatography-tandem mass spectrometry analysis of the
full-length extension products revealed a spectrum of products arising
principally by incorporation of dC or dA opposite M1dG followed by partial or
full-length extension. A greater proportion of -1 deletions were observed when
dT was positioned 5' of M1dG. Two crystal structures were determined, including
a "type II" frameshift deletion complex and another complex with Dpo4 bound to a
dC.M1dG pair located in the postinsertion context. Importantly, M1dG was in the
ring-closed state in both structures, and in the structure with dC opposite
M1dG, the dC residue moved out of the Dpo4 active site, into the minor groove.
The results are consistent with the reported mutagenicity of M1dG and illustrate
how the lesion may affect replication events.
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