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PDBsum entry 2ex3
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Transferase/replication
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PDB id
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2ex3
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Contents |
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(+ 0 more)
570 a.a.
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(+ 0 more)
196 a.a.
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References listed in PDB file
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Key reference
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Title
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The phi29 DNA polymerase:protein-Primer structure suggests a model for the initiation to elongation transition.
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Authors
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S.Kamtekar,
A.J.Berman,
J.Wang,
J.M.Lázaro,
M.De vega,
L.Blanco,
M.Salas,
T.A.Steitz.
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Ref.
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EMBO J, 2006,
25,
1335-1343.
[DOI no: ]
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PubMed id
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Abstract
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The absolute requirement for primers in the initiation of DNA synthesis poses a
problem for replicating the ends of linear chromosomes. The DNA polymerase of
bacteriophage phi29 solves this problem by using a serine hydroxyl of terminal
protein to prime replication. The 3.0 A resolution structure shows one domain of
terminal protein making no interactions, a second binding the polymerase and a
third domain containing the priming serine occupying the same binding cleft in
the polymerase as duplex DNA does during elongation. Thus, the progressively
elongating DNA duplex product must displace this priming domain. Further, this
heterodimer of polymerase and terminal protein cannot accommodate upstream
template DNA, thereby explaining its specificity for initiating DNA synthesis
only at the ends of the bacteriophage genome. We propose a model for the
transition from the initiation to the elongation phases in which the priming
domain of terminal protein moves out of the active site as polymerase elongates
the primer strand. The model indicates that terminal protein should dissociate
from polymerase after the incorporation of approximately six nucleotides.
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Figure 1.
Figure 1 Electron density for a helix of terminal protein near
the active site of polymerase. On the left is a 3.5 Å
resolution map contoured at 1  using
data from the I23 crystal form. It was calculated using
amplitudes sharpened by a factor of 100 and experimentally
phased with solvent-flattened heavy-atom phases. Side chains
cannot be unambiguously assigned in this map. On the right is a
composite omit map contoured at 1 and
calculated to 3 Å using data from the C2 crystal form.
Side chain density is much better defined in this map. Figures
1, 2, 3A, 3B, and 4 were made using Pymol (http://www.pymol.org).
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Figure 2.
Figure 2 The structure of the polymerase:terminal protein
heterodimer. (A) A ribbon representation, with polymerase
colored according to Kamtekar et al, 2004, and terminal protein
shown with cylindrical helices. (B) A view of the complex
rotated 90° from that shown in (A), with terminal protein
shown as cylinders underneath a transparent surface. (C) A C[
 ]trace
of polymerase from the polymerase:terminal protein complex (in
color) superimposed on the apo polymerase structure. Significant
differences in conformation occur only in a loop between
residues 304 and 314 (shown in magenta in the complex and in
black in the apo polymerase structure). The polymerase active
site is marked by the space-filling representations of the
carboxylates that coordinate the catalytic metal ions. (D)
Terminal protein in the same orientation as in (B).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2006,
25,
1335-1343)
copyright 2006.
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