Summary information and primary citation
- PDB-id
-
5tb9;
DSSR-derived features in text and
JSON formats
- Class
- transferase-DNA
- Method
- X-ray (2.49 Å)
- Summary
- Precatalytic ternary complex of human DNA polymerase
beta in closed conformation with gapped DNA substrate
incoming (-)ftc-tp and mn2+.
- Reference
-
Reed AJ, Vyas R, Raper AT, Suo Z (2017): "Structural
Insights into the Post-Chemistry Steps of Nucleotide
Incorporation Catalyzed by a DNA Polymerase." J.
Am. Chem. Soc., 139, 465-471. doi:
10.1021/jacs.6b11258.
- Abstract
- DNA polymerases are essential enzymes that faithfully
and efficiently replicate genomic information.1-3 The
mechanism of nucleotide incorporation by DNA polymerases
has been extensively studied structurally and kinetically,
but several key steps following phosphodiester bond
formation remain structurally uncharacterized due to
utilization of natural nucleotides. It is thought that the
release of pyrophosphate (PP<sub>i</sub>)
triggers reverse conformational changes in a polymerase in
order to complete a full catalytic cycle as well as prepare
for DNA translocation and subsequent incorporation events.
Here, by using the triphosphates of chain-terminating
antiviral drugs lamivudine ((-)3TC-TP) and emtricitabine
((-)FTC-TP), we structurally reveal the correct sequence of
post-chemistry steps during nucleotide incorporation by
human DNA polymerase β (hPolβ) and provide a structural
basis for PP<sub>i</sub> release. These
post-catalytic structures reveal hPolβ in an open
conformation with PP<sub>i</sub> bound in the
active site, thereby strongly suggesting that the reverse
conformational changes occur prior to
PP<sub>i</sub> release. The results also help
to refine the role of the newly discovered third divalent
metal ion for DNA polymerase-catalyzed nucleotide
incorporation. Furthermore, a post-chemistry structure of
hPolβ in the open conformation, following incorporation of
(-)3TC-MP, with a second (-)3TC-TP molecule bound to the
active site in the absence of PP<sub>i</sub>,
suggests that nucleotide binding stimulates
PP<sub>i</sub> dissociation and occurs before
polymerase translocation. Our structural characterization
defines the order of the elusive post-chemistry steps in
the canonical mechanism of a DNA polymerase.
