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PDBsum entry 1qqc
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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 an archaebacterial DNA polymerase.
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Authors
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Y.Zhao,
D.Jeruzalmi,
I.Moarefi,
L.Leighton,
R.Lasken,
J.Kuriyan.
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Ref.
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Structure Fold Des, 1999,
7,
1189-1199.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Members of the Pol II family of DNA polymerases are responsible for
chromosomal replication in eukaryotes, and carry out highly processive DNA
replication when attached to ring-shaped processivity clamps. The sequences of
Pol II polymerases are distinct from those of members of the well-studied Pol I
family of DNA polymerases. The DNA polymerase from the archaebacterium
Desulfurococcus strain Tok (D. Tok Pol) is a member of the Pol II family that
retains catalytic activity at elevated temperatures. RESULTS: The crystal
structure of D. Tok Pol has been determined at 2.4 A resolution. The
architecture of this Pol II type DNA polymerase resembles that of the DNA
polymerase from the bacteriophage RB69, with which it shares less than
approximately 20% sequence identity. As in RB69, the central catalytic region of
the DNA polymerase is located within the 'palm' subdomain and is strikingly
similar in structure to the corresponding regions of Pol I type DNA polymerases.
The structural scaffold that surrounds the catalytic core in D. Tok Pol is
unrelated in structure to that of Pol I type polymerases. The 3'-5' proofreading
exonuclease domain of D. Tok Pol resembles the corresponding domains of RB69 Pol
and Pol I type DNA polymerases. The exonuclease domain in D. Tok Pol is located
in the same position relative to the polymerase domain as seen in RB69, and on
the opposite side of the palm subdomain compared to its location in Pol I type
polymerases. The N-terminal domain of D. Tok Pol has structural similarity to
RNA-binding domains. Sequence alignments suggest that this domain is conserved
in the eukaryotic DNA polymerases delta and epsilon. CONCLUSIONS: The structure
of D. Tok Pol confirms that the modes of binding of the template and extrusion
of newly synthesized duplex DNA are likely to be similar in both Pol II and Pol
I type DNA polymerases. However, the mechanism by which the newly synthesized
product transits in and out of the proofreading exonuclease domain has to be
quite different. The discovery of a domain that seems to be an RNA-binding
module raises the possibility that Pol II family members interact with RNA.
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Figure 6.
Figure 6. Comparison of surface charges in D. Tok Pol and
RB69 Pol. Accessible-surface representation of (a) D. Tok Pol
and (b) RB69 Pol in the same orientation after superposition of
their palm subdomains. Surface regions corresponding to the
terminal oxygen atoms of aspartate and glutamate are colored
red, whereas surface regions contributed by the sidechain
nitrogen of lysines and arginines are colored blue. D. Tok Pol
has a striking pairing of oppositely charged residues not seen
in RB69 pol. A representation of D. Tok Pol as a worm is
included for orientation.
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The above figure is
reprinted
by permission from Cell Press:
Structure Fold Des
(1999,
7,
1189-1199)
copyright 1999.
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