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PDBsum entry 1wns
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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 DNA polymerase from hyperthermophilic archaeon pyrococcus kodakaraensis kod1.
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Authors
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H.Hashimoto,
M.Nishioka,
S.Fujiwara,
M.Takagi,
T.Imanaka,
T.Inoue,
Y.Kai.
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Ref.
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J Mol Biol, 2001,
306,
469-477.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of family B DNA polymerase from the hyperthermophilic
archaeon Pyrococcus kodakaraensis KOD1 (KOD DNA polymerase) was determined. KOD
DNA polymerase exhibits the highest known extension rate, processivity and
fidelity. We carried out the structural analysis of KOD DNA polymerase in order
to clarify the mechanisms of those enzymatic features. Structural comparison of
DNA polymerases from hyperthermophilic archaea highlighted the conformational
difference in Thumb domains. The Thumb domain of KOD DNA polymerase shows an
"opened" conformation. The fingers subdomain possessed many basic
residues at the side of the polymerase active site. The residues are considered
to be accessible to the incoming dNTP by electrostatic interaction. A
beta-hairpin motif (residues 242-249) extends from the Exonuclease (Exo) domain
as seen in the editing complex of the RB69 DNA polymerase from bacteriophage
RB69. Many arginine residues are located at the forked-point (the junction of
the template-binding and editing clefts) of KOD DNA polymerase, suggesting that
the basic environment is suitable for partitioning of the primer and template
DNA duplex and for stabilizing the partially melted DNA structure in the
high-temperature environments. The stabilization of the melted DNA structure at
the forked-point may be correlated with the high PCR performance of KOD DNA
polymerase, which is due to low error rate, high elongation rate and
processivity.
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Figure 1.
Figure 1. (a) Overall structure of
KOD DNA polymerase. The struc-
ture is composed of domains and
subdomains, which are N-terminal
(N-ter, violet), Exonuclease (Exo,
blue), Polymerase (Pol) domain
including the Palm (brown) and
Fingers (green) subdomains and
the Thumb domain (red), including
the Thumb-1 and Thumb-2 subdo-
mains. Conserved carboxylate
residues in Polymerase and Exonu-
clease active site are shown by ball-
and-stick models. (b) Confor-
mational comparison of Thumb
domains among three archaeal
DNA polymerases. Red, KOD
DNA polymerase; blue, Tgo DNA
polymerase; and green, 9°N-7 DNA
polymerase. The comparison shows
that the Thumb domain of KOD
DNA polymerase displays the most
``opened'' conformation.
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Figure 4.
Figure 4. Molecular surface with electrostatic potential
map around the forked-point. The red and blue surfaces
are acidic and basic regions, respectively. Domains and
subdomains are labeled with orange letters. Polymerase
and Exonuclease active sites are labeled with P and E,
respectively. The b-hairpin is labeled with b.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
306,
469-477)
copyright 2001.
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