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PDBsum entry 1s5j
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References listed in PDB file
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Key reference
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Title
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Insights into DNA replication: the crystal structure of DNA polymerase b1 from the archaeon sulfolobus solfataricus.
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Authors
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C.Savino,
L.Federici,
K.A.Johnson,
B.Vallone,
V.Nastopoulos,
M.Rossi,
F.M.Pisani,
D.Tsernoglou.
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Ref.
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Structure, 2004,
12,
2001-2008.
[DOI no: ]
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PubMed id
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Abstract
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To minimize the large number of mispairs during genome duplication owing to the
large amount of DNA to be synthesized, many replicative polymerases have
accessory domains with complementary functions. We describe the crystal
structure of replicative DNA polymerase B1 from the archaeon Sulfolobus
solfataricus. Comparison between other known structures indicates that although
the protein is folded into the typical N-terminal, editing 3'-5'exonuclease, and
C-terminal right-handed polymerase domains, it is characterized by the unusual
presence of two extra alpha helices in the N-terminal domain interacting with
the fingers helices to form an extended fingers subdomain, a structural feature
that can account for some functional features of the protein. We explore the
structural basis of specific lesion recognition, the initial step in DNA repair,
describing how the N-terminal subdomain pocket of archaeal DNA polymerases could
allow specific recognition of deaminated bases such as uracil and hypoxanthine
in addition to the typical DNA bases.
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Figure 4.
Figure 4. Modeling Deminated Bases into the Protein(A)
Uridine5'monophosphate (dUMP). It is possible to see the binding
between the R142 and the sulfate ion that mimics the phosphate
in the 5' position, the hydrogen bonds that fix the position of
R464 and N161 and would be expected to discriminate between
oxygen or amino group, i.e., uracil or cytosine base, and the
position of Y158, which could contribute to steric
discrimination against the thymine methyl group.(B)
Hypoxanthine. The oxygen in position 6 on hypoxanthine could be
recognized in same way as the oxygen in position 4 of uracil.
Only the hypoxanthine nucleoside is shown to highlight the
position of the sulfate ion. The dUMP and the hypoxanthine were
positioned manually to maximize hydrogen bonding and minimize
steric clashes.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2004,
12,
2001-2008)
copyright 2004.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray diffraction studies of DNA polymerase from the thermophilic archaeon sulfolobus solfataricus.
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Authors
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V.Nastopoulos,
F.M.Pisani,
C.Savino,
L.Federici,
M.Rossi,
D.Tsernoglou.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1998,
54,
1002-1004.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. A typical diffraction pattern of a crystal of DNA polymerase
from
Sulfolobus solfataricus. The
edge of frame is at 2.6 A.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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