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PDBsum entry 1waj
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Nucleotidyltransferase
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PDB id
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1waj
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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 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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Abstract
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The 2.8 A resolution crystal structure of the bacteriophage RB69 gp43, a member
of the eukaryotic pol alpha family of replicative DNA polymerases, shares some
similarities with other polymerases but shows many differences. Although its
palm domain has the same topology as other polymerases, except rat DNA
polymerase beta, one of the three carboxylates required for nucleotidyl transfer
is located on a different beta strand. The structures of the fingers and thumb
domains are unrelated to all other known polymerase structures. The editing
3'-5' exonuclease domain of gp43 is homologous to that of E. coli DNA polymerase
I but lies on the opposite side of the polymerase active site. An extended
structure-based alignment of eukaryotic DNA polymerase sequences provides
structural insights that should be applicable to most eukaryotic DNA polymerases.
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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
reprinted
by permission from Cell Press:
Cell
(1997,
89,
1087-1099)
copyright 1997.
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Secondary reference #1
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Title
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Structural basis for phenotypes of mutant pol alpha family DNA polymerases
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Authors
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J.Wang,
T.Steitz.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #2
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Title
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Crystal structures of an nh2-Terminal fragment of t4 DNA polymerase and its complexes with single-Stranded DNA and with divalent metal ions.
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Authors
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J.Wang,
P.Yu,
T.C.Lin,
W.H.Konigsberg,
T.A.Steitz.
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Ref.
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Biochemistry, 1996,
35,
8110-8119.
[DOI no: ]
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PubMed id
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Secondary reference #3
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Title
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Modular organization of t4 DNA polymerase. Evidence from phylogenetics.
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Authors
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C.C.Wang,
L.S.Yeh,
J.D.Karam.
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Ref.
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J Biol Chem, 1995,
270,
26558-26564.
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PubMed id
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Secondary reference #4
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Title
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Primary structure of t4 DNA polymerase. Evolutionary relatedness to eucaryotic and other procaryotic DNA polymerases.
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Authors
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E.K.Spicer,
J.Rush,
C.Fung,
L.J.Reha-Krantz,
J.D.Karam,
W.H.Konigsberg.
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Ref.
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J Biol Chem, 1988,
263,
7478-7486.
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PubMed id
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