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PDBsum entry 1rzt
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Transferase/DNA
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PDB id
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1rzt
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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A structural solution for the DNA polymerase lambda-Dependent repair of DNA gaps with minimal homology.
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Authors
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M.Garcia-Diaz,
K.Bebenek,
J.M.Krahn,
L.Blanco,
T.A.Kunkel,
L.C.Pedersen.
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Ref.
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Mol Cell, 2004,
13,
561-572.
[DOI no: ]
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PubMed id
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Abstract
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Human DNA polymerase lambda (Pol lambda) is a family X member with low
frameshift fidelity that has been suggested to perform gap-filling DNA synthesis
during base excision repair and during repair of broken ends with limited
homology. Here, we present a 2.1 A crystal structure of the catalytic core of
Pol lambda in complex with DNA containing a two nucleotide gap. Pol lambda makes
limited contacts with the template strand at the polymerase active site, and
superimposition with Pol beta in a ternary complex suggests a shift in the
position of the DNA at the active site that is reminiscent of a deletion
intermediate. Surprisingly, Pol lambda can adopt a closed conformation, even in
the absence of dNTP binding. These observations have implications for the
catalytic mechanism and putative DNA repair functions of Pol lambda.
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Figure 4.
Figure 4. Superimposition of Pol λ with the Open and
Closed Conformations of Pol βSuperimposition of the α carbon
trace of human Pol λ (red) with the structures of human Pol β
in an open (1BPX; yellow) and closed (1BPY; blue) conformation.
The roman numerals refer to different regions of the Pol λ
structure as indicated in the text. The rms deviation was 1.4
Å for 112 C-α atoms for 1BPX and 1.4 Å for 113 C-α
atoms for 1BPY.
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Figure 7.
Figure 7. Biological Implications of the Pol λ
Structure(A) Stereo view of an overlay of the active site of Pol
λ with that of Pol β in a closed conformation (1BPY). The DNA
corresponds to the Pol λ structure, while the incoming ddCTP
(green) and metal ions (gray balls) correspond to Pol β 1BPY.
Relevant residues are shown in red (Pol λ) and blue (Pol β).
The template strand is gray and the primer terminus is
yellow.(B) Electrostatic surface potential of Pol λ and Pol β.
The DNA for each of the structures is shown in gray (template)
and yellow (primer and downstream primer). The potential ranges
from −8 kT/e (red) to 8 kT/e (blue).
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(2004,
13,
561-572)
copyright 2004.
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