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PDBsum entry 3mgi
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Lyase,transferase/DNA
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PDB id
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3mgi
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References listed in PDB file
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Key reference
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Title
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Loop 1 modulates the fidelity of DNA polymerase lambda.
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Authors
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K.Bebenek,
M.Garcia-Diaz,
R.Z.Zhou,
L.F.Povirk,
T.A.Kunkel.
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Ref.
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Nucleic Acids Res, 2010,
38,
5419-5431.
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PubMed id
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Abstract
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Differences in the substrate specificity of mammalian family X DNA polymerases
are proposed to partly depend on a loop (loop 1) upstream of the polymerase
active site. To examine if this is the case in DNA polymerase lambda (pol
lambda), here we characterize a variant of the human polymerase in which nine
residues of loop 1 are replaced with four residues from the equivalent position
in pol beta. Crystal structures of the mutant enzyme bound to gapped DNA with
and without a correct dNTP reveal that the change in loop 1 does not affect the
overall structure of the protein. Consistent with these structural data, the
mutant enzyme has relatively normal catalytic efficiency for correct
incorporation, and it efficiently participates in non-homologous end joining of
double-strand DNA breaks. However, DNA junctions recovered from end-joining
reactions are more diverse than normal, and the mutant enzyme is substantially
less accurate than wild-type pol lambda in three different biochemical assays.
Comparisons of the binary and ternary complex crystal structures of mutant and
wild-type pol lambda suggest that loop 1 modulates pol lambda's fidelity by
controlling dNTP-induced movements of the template strand and the
primer-terminal 3'-OH as the enzyme transitions from an inactive to an active
conformation.
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