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PDBsum entry 1zjn
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DNA/lyase/transferase
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PDB id
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1zjn
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References listed in PDB file
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Key reference
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Title
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Nucleotide-Induced DNA polymerase active site motions accommodating a mutagenic DNA intermediate.
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Authors
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V.K.Batra,
W.A.Beard,
D.D.Shock,
L.C.Pedersen,
S.H.Wilson.
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Ref.
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Structure (Camb), 2005,
13,
1225-1233.
[DOI no: ]
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PubMed id
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Abstract
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DNA polymerases occasionally insert the wrong nucleotide. For this error to
become a mutation, the mispair must be extended. We report a structure of DNA
polymerase beta (pol beta) with a DNA mismatch at the boundary of the polymerase
active site. The structure of this complex indicates that the templating adenine
of the mispair stacks with the primer terminus adenine while the templating
(coding) cytosine is flipped out of the DNA helix. Soaking the crystals of the
binary complex with dGTP resulted in crystals of a ternary substrate complex. In
this case, the templating cytosine is observed within the DNA helix and forms
Watson-Crick hydrogen bonds with the incoming dGTP. The adenine at the primer
terminus has rotated into a syn-conformation to interact with the opposite
adenine in a planar configuration. Yet, the 3'-hydroxyl on the primer terminus
is out of position for efficient nucleotide insertion.
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Figure 4.
Figure 4. Structural Comparison of the Binary DNA and
Ternary Substrate Complexes of DNA Polymerase b with an A-A
Mismatch at the Boundary of the Active Site
A comparison of
the polymerase and DNA conformations near the polymerase active
site in the crystallographic structures of the binary (blue) and
ternary (green) complexes with an A-A mismatch (yellow) at the
primer terminus. As with matched termini, the N subdomain is
observed to be open in the binary complex and closed in the
ternary complex. Three striking conformational changes in the
DNA are observed in forming the closed ternary substrate
complex: (1) the adenine at the primer terminus rotates into a
syn-conformation; (2) this permits the templating adenine of the
mismatch to reposition itself opposite the primer terminus (n
-1); (3) the coding template cytosine (orange) flips into the
DNA helix, thereby forming Watson-Crick hydrogen bonds with the
incoming dGTP (orange).
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The above figure is
reprinted
by permission from Cell Press:
Structure (Camb)
(2005,
13,
1225-1233)
copyright 2005.
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