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PDBsum entry 2r8k
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Replication, transferase/DNA
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PDB id
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2r8k
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References listed in PDB file
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Key reference
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Title
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Bypass of DNA lesions generated during anticancer treatment with cisplatin by DNA polymerase eta.
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Authors
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A.Alt,
K.Lammens,
C.Chiocchini,
A.Lammens,
J.C.Pieck,
D.Kuch,
K.P.Hopfner,
T.Carell.
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Ref.
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Science, 2007,
318,
967-970.
[DOI no: ]
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PubMed id
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Abstract
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DNA polymerase eta (Pol eta) is a eukaryotic lesion bypass polymerase that helps
organisms to survive exposure to ultraviolet (UV) radiation, and tumor cells to
gain resistance against cisplatin-based chemotherapy. It allows cells to
replicate across cross-link lesions such as 1,2-d(GpG) cisplatin adducts (Pt-GG)
and UV-induced cis-syn thymine dimers. We present structural and biochemical
analysis of how Pol eta copies Pt-GG-containing DNA. The damaged DNA is bound in
an open DNA binding rim. Nucleotidyl transfer requires the DNA to rotate into an
active conformation, driven by hydrogen bonding of the templating base to the
dNTP. For the 3'dG of the Pt-GG, this step is accomplished by a Watson-Crick
base pair to dCTP and is biochemically efficient and accurate. In contrast,
bypass of the 5'dG of the Pt-GG is less efficient and promiscuous for dCTP and
dATP as a result of the presence of the rigid Pt cross-link. Our analysis
reveals the set of structural features that enable Pol eta to replicate across
strongly distorting DNA lesions.
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Figure 1.
Fig. 1. Pol  structure in
ternary complex with lesion containing DNA. (A) In the 3'dG
elongation complex, the cisplatin (magenta) is shown with the
platinum anomalous electron density contoured at 10  .
The primer and template strands of the DNA (brown) and the
Watson-Crick H-bonded dCTP (magenta) are depicted as sticks. The
two metal ions are shown as gray spheres. (B) View of the
1,2-d(GpG) cisplatin lesion superimposed with the simulated
annealed composit-omit density map contoured at 1.0 sigma. (C)
The catalytic residues in the active site. R73 orients the dCTP
for H-bonding with the 3'desoxyguanine of the lesion. (D)
Schematics of protein-DNA contacts representing the
pre-elongation, 3'dG elongation, and 5'dG elongation complex.
Direct hydrogen-bonds are indicated by solid lines. DNA contacts
with the symmetry-related molecule are not shown.
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Figure 2.
Fig. 2. The 3'dG elongation process of Pol (A) The catalytic
residues, the metal ions and the dCTP are shown for the
pre-elongation complex. Phe^35 stacks upon the dNTPs
deoxyribose. The dNTP is unpaired. (B) Detailed view of the
lesion in the pre-elongation complex (cyan) superpositioned with
the lesion in the 3'dG elongation state (magenta). For clarity,
the finger domain has been omitted and the DNA molecules (cyan
and magenta) are viewed in a simplified form. Watson-Crick base
pairing revolves the DNA to position the 3'OH of the primer for
nucleophilic attack on the  -phosphate of the
dNTP. (C) The DNA revolves from the pre-elongation state into
the first elongation state, forming a Watson-Crick base pair.
This aligns the 3'OH of the primer for nucleotidyl transfer. The
protein of the pre-elongation complex is omitted for clarity,
and the protein of the 3'dG elongation state is depicted in
gray. The DNA molecules are color coded as in Fig. 2B.
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The above figures are
reprinted
by permission from the AAAs:
Science
(2007,
318,
967-970)
copyright 2007.
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