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PDBsum entry 1ig9
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Transferase/DNA
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PDB id
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1ig9
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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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Structure of the replicating complex of a pol alpha family DNA polymerase.
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Authors
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M.C.Franklin,
J.Wang,
T.A.Steitz.
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Ref.
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Cell, 2001,
105,
657-667.
[DOI no: ]
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PubMed id
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Abstract
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We describe the 2.6 A resolution crystal structure of RB69 DNA polymerase with
primer-template DNA and dTTP, capturing the step just before primer extension.
This ternary complex structure in the human DNA polymerase alpha family shows a
60 degrees rotation of the fingers domain relative to the apo-protein structure,
similar to the fingers movement in pol I family polymerases. Minor groove
interactions near the primer 3' terminus suggest a common fidelity mechanism for
pol I and pol alpha family polymerases. The duplex product DNA orientation
differs by 40 degrees between the polymerizing mode and editing mode structures.
The role of the thumb in this DNA motion provides a model for editing in the pol
alpha family.
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Figure 2.
Figure 2. The Polymerase Active Site(A) The backbones of
the polymerase palm and fingers domains are shown as magenta and
blue ribbons. The carbon atoms of the polymerase side chains
shown in stick form are white, while those of the DNA template
are dark gray, and those of the primer DNA and dTTP are gold.
The bound calcium atoms are shown as light blue mesh spheres,
labeled A and B according to their catalytic function. Hydrogen
bonds are shown as green lines, while interactions with the
metal ions are blue lines. This view looks down the length of
the fingers, roughly 180° away from the orientation of
Figure 1A.(B) The KKRY motif (residues 705–708) interacts with
the primer-template duplex next to the polymerase active site.
Residues 703–708 are shown; Thr 703 and Gly 704 are not
conserved in the pol α family. Asp 621 from Figure 2A is shown
as an isolated side chain. Only the last two bases of the primer
strand are shown for clarity. The orientation of this figure can
be related to that of Figure 2A by comparing the primer-template
DNA
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Figure 4.
Figure 4. A Tunnel into the Polymerase Active SiteThe
molecular surface of RB69 pol in its polymerizing mode is
colored by domain according to the scheme of Figure 1A. The dTTP
and associated metal ions are at the center of the image, with
the primer-template DNA, shown semitransparently behind the
surface, extending off to the left. The terminal amine of Lys
560 protrudes into the tunnel, as indicated. This view is
roughly the same as that of Figure 2 and Figure 3
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
105,
657-667)
copyright 2001.
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Secondary reference #1
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Title
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Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage rb69.
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Authors
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J.Wang,
A.K.Sattar,
C.C.Wang,
J.D.Karam,
W.H.Konigsberg,
T.A.Steitz.
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Ref.
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Cell, 1997,
89,
1087-1099.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. Stereo Representation of a Portion of Two
Electron-Density MapsThe experimental (blue at 1.5σ) and
2F[o]-F[c] (pink at 1.25σ) densities of RB69 gp43 at 2.8
Å resolution are superimposed on the refined model in the
region around D621 in the polymerase catalytic site.
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Figure 8.
Figure 8. Solvent-Accessible Contact-Surface Representation
of a Hypothetical Model for the Replication ComplexIncluded in
the model are gp32, gp43, gp45, and a model-built DNA primer
template bound with its 3′ terminus in the exonuclease active
site. The protein coordinates used were from the crystal
structures of T4 gp32 core ([62]), the β subunit of E. coli DNA
polymerase III ( [39]), and RB69 gp43. The locations of the
various domains and clefts are indicated by arrows.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex.
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Authors
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Y.Shamoo,
T.A.Steitz.
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Ref.
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Cell, 1999,
99,
155-166.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Peptide Interactions with the Sliding ClampThe
interaction of pol-CT with RB69 sliding clamp is close fitting
and consists mainly of hydrophobic interactions. Accessible
surface of RB69 sliding clamp is shown in blue, while pol-CT is
displayed as a stick model. To illustrate the pol-CT-binding
pocket, all the sliding clamp surfaces within 4.5 Å of the
pol-CT model are colored in yellow. The figure was made using
GRASP ([37]).
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Figure 4.
Figure 4. Residues of the T4 and RB69 Pol-CTs that Are
Similar to the ClampResidues in the RB69 pol-CT that are colored
in blue are different in the T4 pol-CT. Residues that are the
same in T4 and RB69 are shown in red. Residues that differ point
away from the pol-CT-binding pocket (Table 1).
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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