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PDBsum entry 1tva
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Transferase/DNA
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PDB id
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1tva
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References listed in PDB file
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Key reference
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Title
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Structural insights into DNA polymerase beta deterrents for misincorporation support an induced-Fit mechanism for fidelity.
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Authors
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J.M.Krahn,
W.A.Beard,
S.H.Wilson.
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Ref.
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Structure, 2004,
12,
1823-1832.
[DOI no: ]
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PubMed id
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Abstract
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DNA polymerases generally select the correct nucleotide from a pool of
structurally similar molecules to preserve Watson-Crick base-pairing rules. We
report the structure of DNA polymerase beta with DNA mismatches situated in the
polymerase active site. This was achieved by using nicked product DNA that traps
the mispair (template-primer, A-C or T-C) in the nascent base pair binding
pocket. The structure of each mispair complex indicates that the bases do not
form hydrogen bonds with one another, but form a staggered arrangement where the
bases of the mispair partially overlap. This prevents closure/opening of the N
subdomain that is believed to be required for catalytic cycling. The partially
open conformation of the N subdomain results in distinct hydrogen bonding
networks that are unique for each mispair. These structures define diverse
molecular aspects of misinsertion that are consistent with the induced-fit model
for substrate specificity.
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Figure 6.
Figure 6. Comparison of Alternate DNA and N-Subdomain
ConformationsThe conformation of the N subdomain, as monitored
by the position of a helix N, for the NAC mismatch structure
(green) is in an intermediate position relative to the active
closed (blue; Protein Data Bank entry 1BPY) or inactive open
(red; Protein Data Bank entry 1BPX) conformations. These
structures were superimposed using the C subdomains. The
template strand is displaced to a greater extent than that
observed for the open binary DNA complex relative to the closed
ternary complex. The position of a helix N and the template
strand in the open nicked complex (not shown; Protein Data Bank
entry 1BPZ) is identical to that illustrated for the open
complex.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2004,
12,
1823-1832)
copyright 2004.
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