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PDBsum entry 1s0m
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Transferase/DNA
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PDB id
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1s0m
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase.
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Authors
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H.Ling,
J.M.Sayer,
B.S.Plosky,
H.Yagi,
F.Boudsocq,
R.Woodgate,
D.M.Jerina,
W.Yang.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
2265-2269.
[DOI no: ]
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PubMed id
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Abstract
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The first occupation-associated cancers to be recognized were the sooty warts
(cancers of the scrotum) suffered by chimney sweeps in 18th century England. In
the 19th century, high incidences of skin cancers were noted among fuel industry
workers. By the early 20th century, malignant skin tumors were produced in
laboratory animals by repeatedly painting them with coal tar. The culprit in
coal tar that induces cancer was finally isolated in 1933 and determined to be
benzo[a]pyrene (BP), a polycyclic aromatic hydrocarbon. A residue of fuel and
tobacco combustion and frequently ingested by humans, BP is metabolized in
mammals to benzo[a]pyrene diol epoxide (BPDE), which forms covalent DNA adducts
and induces tumor growth. In the 70 yr since its isolation, BP has been the most
studied carcinogen. Yet, there has been no crystal structure of a BPDE DNA
adduct. We report here the crystal structure of a BPDE-adenine adduct
base-paired with thymine at a template-primer junction and complexed with the
lesion-bypass DNA polymerase Dpo4 and an incoming nucleotide. Two conformations
of the BPDE, one intercalated between base pairs and another solvent-exposed in
the major groove, are observed. The latter conformation, which can be stabilized
by organic solvents that reduce the dielectric constant, seems more favorable
for DNA replication by Dpo4. These structures also suggest a mechanism by which
mutations are generated during replication of DNA containing BPDE adducts.
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Figure 2.
Fig. 2. Crystal structures of BP-1 and BP-2. Dpo4 is
represented by a purple molecular surface, the DNA and the
incoming dATP are shown as blue sticks, and the PAH is
highlighted in yellow. The divalent cations (Ca^2+) are shown as
green spheres. The unpaired dAMP at the 3' end of the template
strand was added by the terminal deoxynucleotide transferase
(TdT) activity of Dpo4 that is common to archael D in B-like
polymerases (34) (Fig. 4, which is published as supporting
information on the PNAS web site). Figs. 2 and 3 were generated
by using RIBBONS and GRASP (35, 36).
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Figure 3.
Fig. 3. Distortion of DNA by the BPDE adduct. (A)
Comparison of the crystal and NMR structures. The dA*·dT
and the surrounding base pairs including the replicating base
pair are shown as ball-and-stick models. The crystal structures
are shown with the F[o] - F[c] omit electron density maps
contoured at 1.0  in blue. The carbon,
oxygen, nitrogen, and phosphorus atoms are colored yellow, red,
blue, and purple, respectively. (B) Hydrogen bond formation at
dA*·dT and the adjacent replicating base pair
dT·dATP. Looking down the DNA helical axis, the two
layers of the base pair and the PAH adduct are shown, purple for
the replicating base pair, gold for the dA* adduct, and green
for its partner dT. The incoming nucleotide in BP-1 is in the
syn conformation. In the BP-2 complex, where the PAH is in the
major groove, the adenine base of the dA* is shifted to the
major groove, disrupting the normal hydrogen bonds with its
partner, dT. The location of a normal dA is modeled in gray. (C)
Stereo view of the overlay of the DNA structures from BP-1
(blue) and BP-2 (gold) after superimposition of the Dpo4
structures. With the PAH intercalated, the base pair ladder in
the BP-1 complex is shifted by one register compared with that
in the BP-2 complex.
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