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PDBsum entry 2fms
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Transferase/DNA
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PDB id
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2fms
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References listed in PDB file
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Key reference
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Title
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Magnesium-Induced assembly of a complete DNA polymerase catalytic complex.
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Authors
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V.K.Batra,
W.A.Beard,
D.D.Shock,
J.M.Krahn,
L.C.Pedersen,
S.H.Wilson.
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Ref.
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Structure, 2006,
14,
757-766.
[DOI no: ]
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PubMed id
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Abstract
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The molecular details of the nucleotidyl transferase reaction have remained
speculative, as strategies to trap catalytic intermediates for structure
determination utilize substrates lacking the primer terminus 3'-OH and catalytic
Mg2+, resulting in an incomplete and distorted active site geometry. Since the
geometric arrangement of these essential atoms will impact chemistry, structural
insight into fidelity strategies has been hampered. Here, we present a crystal
structure of a precatalytic complex of a DNA polymerase with bound substrates
that include the primer 3'-OH and catalytic Mg2+. This catalytic intermediate
was trapped with a nonhydrolyzable deoxynucleotide analog. Comparison with two
new structures of DNA polymerase beta lacking the 3'-OH or catalytic Mg2+ is
described. These structures provide direct evidence that both atoms are required
to achieve a proper geometry necessary for an in-line nucleophilic attack of O3'
on the alphaP of the incoming nucleotide.
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Figure 7.
Figure 7. Stereoview of the Pol b Active Site
Superimposed structures of pol b with either Na^+ (light blue)
or Mg2+ (yellow) in the catalytic metal site A. Residues that
hydrogen bond (green) to the triphosphate moiety of the incoming
nucleotide and the active site aspartates are shown. When Na^+
occupies the catalytic metal site, O3' of the primer terminus is
3.5 and 4.7 Å from the catalytic metal and aP of the incoming
nucleotide, respectively. In contrast, with Mg2+ in the
catalytic metal site, an altered sugar pucker positions O3' of
the primer terminus 2.2 and 3.4 Å from the catalytic metal and
Pa of the incoming nucleotide, respectively.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2006,
14,
757-766)
copyright 2006.
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