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PDBsum entry 1kej
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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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Crystal structures of a template-Independent DNA polymerase: murine terminal deoxynucleotidyltransferase.
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Authors
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M.Delarue,
J.B.Boulé,
J.Lescar,
N.Expert-Bezançon,
N.Jourdan,
N.Sukumar,
F.Rougeon,
C.Papanicolaou.
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Ref.
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EMBO J, 2002,
21,
427-439.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the catalytic core of murine terminal
deoxynucleotidyltransferase (TdT) at 2.35 A resolution reveals a typical DNA
polymerase beta-like fold locked in a closed form. In addition, the structures
of two different binary complexes, one with an oligonucleotide primer and the
other with an incoming ddATP-Co(2+) complex, show that the substrates and the
two divalent ions in the catalytic site are positioned in TdT in a manner
similar to that described for the human DNA polymerase beta ternary complex,
suggesting a common two metal ions mechanism of nucleotidyl transfer in these
two proteins. The inability of TdT to accommodate a template strand can be
explained by steric hindrance at the catalytic site caused by a long lariat-like
loop, which is absent in DNA polymerase beta. However, displacement of this
discriminating loop would be sufficient to unmask a number of evolutionarily
conserved residues, which could then interact with a template DNA strand. The
present structure can be used to model the recently discovered human polymerase
mu, with which it shares 43% sequence identity.
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Figure 1.
Figure 1 General structure and domain organization of TdT. (A)
Linear arrangement of the different domains of C-TdT (blue),
compared with pol  .
The two motifs C and A and the two HhH consensus sequences are
indicated in red and green, respectively. The disordered part of
C-TdT in the crystal is in cyan and the N-terminal extension of
C-TdT compared with pol is
in magenta. The part of the molecule absent from the
crystallized construct is in white. (B) General architecture of
the TdT structure drawn with Molscript (Kraulis, 1991). The
three catalytic aspartate residues are shown in ball-and-stick
representation. The N- and C-termini are in dark blue, while the
two strictly conserved stretches of sequences implicated in the
binding of the incoming dNTP are in cyan and magenta. Loop1 is
shown in yellow. An intrinsic magnesium ion (grey) as well as
the two putative sodium ions bound to the HhH motifs are
represented in CPK mode (blue); only the Na^+ ion with ligands
in an octahedral geometry is labelled.
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Figure 3.
Figure 3 C-TdT is in a closed form. Stereo view of the
superimposed C[  ]traces
of TdT (red) with the closed form of pol (blue).
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2002,
21,
427-439)
copyright 2002.
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