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PDBsum entry 3epg
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Transferase/DNA
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PDB id
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3epg
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References listed in PDB file
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Key reference
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Title
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Lesion bypass of n2-Ethylguanine by human DNA polymerase iota.
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Authors
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M.G.Pence,
P.Blans,
C.N.Zink,
T.Hollis,
J.C.Fishbein,
F.W.Perrino.
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Ref.
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J Biol Chem, 2009,
284,
1732-1740.
[DOI no: ]
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PubMed id
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Abstract
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Nucleotide incorporation and extension opposite N2-ethyl-Gua by DNA polymerase
iota was measured and structures of the DNA polymerase iota-N2-ethyl-Gua complex
with incoming nucleotides were solved. Efficiency and fidelity of DNA polymerase
iota opposite N2-ethyl-Gua was determined by steady state kinetic analysis with
Mg2+ or Mn2+ as the activating metal. DNA polymerase iota incorporates dCMP
opposite N2-ethyl-Gua and unadducted Gua with similar efficiencies in the
presence of Mg2+ and with greater efficiencies in the presence of Mn2+. However,
the fidelity of nucleotide incorporation by DNA polymerase iota opposite
N2-ethyl-Gua and Gua using Mn2+ is lower relative to that using Mg2+ indicating
a metal-dependent effect. DNA polymerase iota extends from the N2-ethyl-Gua:Cyt
3' terminus more efficiently than from the Gua:Cyt base pair. Together these
kinetic data indicate that the DNA polymerase iota catalyzed reaction is well
suited for N(2)-ethyl-Gua bypass. The structure of DNA polymerase iota with
N2-ethyl-Gua at the active site reveals the adducted base in the syn
configuration when the correct incoming nucleotide is present. Positioning of
the ethyl adduct into the major groove removes potential steric overlap between
the adducted template base and the incoming dCTP. Comparing structures of DNA
polymerase iota complexed with N2-ethyl-Gua and Gua at the active site suggests
movements in the DNA polymerase iota polymerase-associated domain to accommodate
the adduct providing direct evidence that DNA polymerase iota efficiently
replicates past a minor groove DNA adduct by positioning the adducted base in
the syn configuration.
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Figure 2.
The structures of DNA pol ι·N^2-ethyl-Gua Complexes
with incoming dCTP or dTTP. A, the structure of DNA pol ι
containing N^2-ethyl-Gua and incoming dCTP shows the
N^2-ethyl-Gua base rotated into the syn configuration. B, the
structure of DNA pol ι containing N^2-ethyl-Gua and incoming
dTTP shows the N^2-ethyl-Gua base in the anti configuration and
the N^2-adduct protruding into the minor groove. C, electron
density around the N^2-ethyl adduct and incoming dCTP. D,
electron density around the N^2-ethyl adduct and the γ
phosphate of the incoming dTTP.
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Figure 4.
Repositioning of Lys^309 in the structure of DNA pol ι with
N^2-ethyl-Gua in the syn configuration. A, the Lys^309 side
chain in DNA pol ι in complex with N^2-ethyl-Gua (green) in the
syn configuration shifts ∼9Å relative to the position of
Lys^309 in DNA pol ι complexed with syn Gua (PDB code 2ALZ,
magenta). B, with N^2-ethyl-Gua in the anti conformation (blue)
Lys^309 remains in a similar position relative to the Lys^309 in
the DNA pol ι·Gua complex (PDB code 2FLP, yellow).
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2009,
284,
1732-1740)
copyright 2009.
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