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PDBsum entry 1tgo
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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 structure of a thermostable type b DNA polymerase from thermococcus gorgonarius.
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Authors
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K.P.Hopfner,
A.Eichinger,
R.A.Engh,
F.Laue,
W.Ankenbauer,
R.Huber,
B.Angerer.
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Ref.
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Proc Natl Acad Sci U S A, 1999,
96,
3600-3605.
[DOI no: ]
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PubMed id
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Abstract
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Most known archaeal DNA polymerases belong to the type B family, which also
includes the DNA replication polymerases of eukaryotes, but maintain high
fidelity at extreme conditions. We describe here the 2.5 A resolution crystal
structure of a DNA polymerase from the Archaea Thermococcus gorgonarius and
identify structural features of the fold and the active site that are likely
responsible for its thermostable function. Comparison with the mesophilic B type
DNA polymerase gp43 of the bacteriophage RB69 highlights thermophilic
adaptations, which include the presence of two disulfide bonds and an enhanced
electrostatic complementarity at the DNA-protein interface. In contrast to gp43,
several loops in the exonuclease and thumb domains are more closely packed; this
apparently blocks primer binding to the exonuclease active site. A physiological
role of this "closed" conformation is unknown but may represent a polymerase
mode, in contrast to an editing mode with an open exonuclease site. This
archaeal B DNA polymerase structure provides a starting point for
structure-based design of polymerases or ligands with applications in
biotechnology and the development of antiviral or anticancer agents.
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Figure 1.
Fig. 1. Stereorepresentation of the electron-density map.
The 2 (F[o]  F[c])
electron density contoured at 1.0  at the
polymerase active site is well defined for the refined model
(stick representation).
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Figure 4.
Fig. 4. Polymerase active site. (A) Stereoribbon
representation (using color code as in Fig. 2) with modeled DNA.
Active-site residues are shown as ball-and-stick representations
with carbon (green), nitrogen (blue), and oxygen (red) atoms.
The DNA template (light brown), primer (light brown), and dNTP
(orange) complex has been taken from the coordinates of T7
replication complex (15) by superimposing D404, D542, and
adjacent residues with corresponding residues in T7 pol (D475
and D654). Phosphorus atoms are yellow. The two metals of the T7
replication complex are shown as magenta spheres. (B)
Experimentally observed metal-binding site for Mn^2+ (F[o] F[c]
density contoured at 5 ) and Zn^2+
in the "low salt" crystal form. The carboxylates E578 and E580
are conserved in type B polymerases (Fig. 3).
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