 |
PDBsum entry 2ibk
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transferase/DNA
|
PDB id
|
|
|
|
2ibk
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
A structural gap in dpo4 supports mutagenic bypass of a major benzo[a]pyrene dg adduct in DNA through template misalignment.
|
|
|
Authors
|
|
J.Bauer,
G.Xing,
H.Yagi,
J.M.Sayer,
D.M.Jerina,
H.Ling.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2007,
104,
14905-14910.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Abstract
|
|
|
Erroneous replication of lesions in DNA by DNA polymerases leads to elevated
mutagenesis. To understand the molecular basis of DNA damage-induced
mutagenesis, we have determined the x-ray structures of the Y-family polymerase,
Dpo4, in complex with a DNA substrate containing a bulky DNA lesion and incoming
nucleotides. The DNA lesion is derived from an environmentally widespread
carcinogenic polycyclic aromatic hydrocarbon, benzo[a]pyrene (BP). The potent
carcinogen BP is metabolized to diol epoxides that form covalent adducts with
cellular DNA. In the present study, the major BP diol epoxide adduct in DNA,
BP-N(2)-deoxyguanosine (BP-dG), was placed at a template-primer junction. Three
ternary complexes reveal replication blockage, extension past a mismatched
lesion, and a -1 frameshift mutation. In the productive structures, the bulky
adduct is flipped/looped out of the DNA helix into a structural gap between the
little finger and core domains. Sequestering of the hydrophobic BP adduct in
this new substrate-binding site permits the DNA to exhibit normal geometry for
primer extension. Extrusion of the lesion by template misalignment allows the
base 5' to the adduct to serve as the template, resulting in a -1 frameshift.
Subsequent strand realignment produces a mismatched base opposite the lesion.
These structural observations, in combination with replication and mutagenesis
data, suggest a model in which the additional substrate-binding site stabilizes
the extrahelical nucleotide for lesion bypass and generation of base
substitutions and -1 frameshift mutations.
|
|
|
|
|
|
|
|
Figure 2.
Structures of BPG-1A, BPG-1B and BPG-2. (A–C) Dpo4 is
represented as a molecular surface with the polymerase core in
cyan and the LF domain in purple; DNA and nucleotide are shown
as sticks, and BP–dG is highlighted in orange. BPG-1B and
BPG-2 in B and C are rotated 180° relative to BPG-1A in A
around the DNA helix axis, to show the extrahelical BP–dG in
the gap between the core and LF domains. (D–F) The DNA
conformations corresponding to (A–C) as stick models, all with
the same orientations as in A. The primer strands are in gray,
and incoming dATP is in pink. The single-stranded portion of the
template DNA is not shown. Figs. 2, 3, and 4 were generated by
using PYMOL (46).
|
|
Figure 4.
Close-up views of BP–dG in the structure gap between the
core and the LF domains. (A) BPG-1B. (B) BPG-2. The protein is
in ribbon models covered by a transparent molecular surface. The
key residues interacting with the adduct G* are shown as stick
models. The BP ring system is in van der Waals contact with the
LF domain (purple); the adducted G base interacts with the core
domain (cyan). The glycerol molecule is in gray.
|
|
|
|
|
|
|
|
|
|
