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PDBsum entry 2faq
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Hydrolase/transferase
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PDB id
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2faq
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References listed in PDB file
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Key reference
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Title
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Atomic structure and nonhomologous end-Joining function of the polymerase component of bacterial DNA ligase d.
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Authors
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H.Zhu,
J.Nandakumar,
J.Aniukwu,
L.K.Wang,
M.S.Glickman,
C.D.Lima,
S.Shuman.
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Ref.
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Proc Natl Acad Sci U S A, 2006,
103,
1711-1716.
[DOI no: ]
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PubMed id
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Abstract
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DNA ligase D (LigD) is a large polyfunctional protein that participates in a
recently discovered pathway of nonhomologous end-joining in bacteria. LigD
consists of an ATP-dependent ligase domain fused to a polymerase domain (Pol)
and a phosphoesterase module. The Pol activity is remarkable for its dependence
on manganese, its ability to perform templated and nontemplated primer extension
reactions, and its preference for adding ribonucleotides to blunt DNA ends. Here
we report the 1.5-A crystal structure of the Pol domain of Pseudomonas LigD and
its complexes with manganese and ATP/dATP substrates, which reveal a minimized
polymerase with a two-metal mechanism and a fold similar to that of archaeal DNA
primase. Mutational analysis highlights the functionally relevant atomic
contacts in the active site. Although distinct nucleoside conformations and
contacts for ATP versus dATP are observed in the cocrystals, the functional
analysis suggests that the ATP-binding mode is the productive conformation for
dNMP and rNMP incorporation. We find that a mutation of Mycobacterium LigD that
uniquely ablates the polymerase activity results in increased fidelity of
blunt-end double-strand break repair in vivo by virtue of eliminating nucleotide
insertions at the recombination junctions. Thus, LigD Pol is a direct catalyst
of mutagenic nonhomologous end-joining in vivo. Our studies underscore a
previously uncharacterized role for the primase-like polymerase family in DNA
repair.
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Figure 2.
Fig. 2. Structure of the LigD Pol domain. The overall fold
of the Pol domain of Pseudomonas LigD is depicted as a ribbon
diagram with  -helices colored
magenta and  -strands colored green.
The N and C termini are indicated. ATP is bound within a cleft
formed by two central -sheets; the cleft is
viewed from the side in A and from above in B.
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Figure 4.
Fig. 4. Active site of LigD Pol. Stereo views are shown of
the active site constituents of the apoenzyme (A), the Mn-ATP
cocrystal (B), and the Mn-dATP cocrystal (C). Potential
hydrogen-bonding interactions are denoted by dashed lines.
Manganese ions and waters are rendered as blue and red spheres,
respectively. Amino acids and sulfate (A), ATP (B), or dATP (C)
ligands are labeled and shown in stick representation.
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