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PDBsum entry 5ktq
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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 the klenow fragment of thermus aquaticus DNA polymerase i complexed with deoxyribonucleoside triphosphates.
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Authors
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Y.Li,
Y.Kong,
S.Korolev,
G.Waksman.
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Ref.
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Protein Sci, 1998,
7,
1116-1123.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structures of the Klenow fragment of the Thermus aquaticus DNA
polymerase I (Klentaq1) complexed with four deoxyribonucleoside triphosphates
(dNTP) have been determined to 2.5 A resolution. The dNTPs bind adjacent to the
O helix of Klentaq1. The triphosphate moieties are at nearly identical positions
in all four complexes and are anchored by three positively charged residues,
Arg659, Lys663, and Arg587, and by two polar residues, His639 and Gln613. The
configuration of the base moieties in the Klentaq1/dNTP complexes demonstrates
variability suggesting that dNTP binding is primarily determined by recognition
and binding of the phosphate moiety. However, when superimposed on the Taq
polymerase/blunt end DNA complex structure (Eom et al., 1996), two of the
dNTP/Klentaq1 structures demonstrate appropriate stacking of the nucleotide base
with the 3' end of the DNA primer strand, suggesting that at least in these two
binary complexes, the observed dNTP conformations are functionally relevant.
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Figure 2.
Fig. 2. A: Schematic representation of the secondary structure of
Klentaql bound with dAW. The small vestigial 3â-5â exonuclease domain
is shown in yellow and the polymerase domaiins shown in green. The
secondarys tructure elements are labeled according to the notation of
Ollise t al. (1985). The helix 0 is shown in blue and tdhAeT P
molecule in red. The side chains of the three carboxylates, Asp610,
Asp785, Asp786, which form the catalytic core are shown in
purple. This figure was prepared using MOLSCRIPT and RASTER3D (Merritt
8c Murphy, 1994; Kraulis, 1991). B: Superimposition of the binary
complex of Klentaql bound to dCTP (this work; in purple) with the
binary complex of E. coli Klenow Pol I bound to dCTP ((Beese et al.,
1993); in pink). C Superimposition of d N T P s in the four
Klentaql/dNTP binary complexes. The binary complexoefs Klentaql with
dATP (green), dTTP (yellow), dCTP
(magenta), dGTP (cyan) were superimposed. The positions of the
triphosphaotef st he dNTP in the four complexa re nearly identical,
while those for the sugar and base differ. The orientation of the side
chain of Qr671 also differs in the four binary complexes. D:
Superimposition of the Klentaql/dCTP binary complex structure (in
purple) with the Taq/DNA complex structure of Eom et al.
(1996) (in yellow for the protein, and white and blue for the
template/primer DNA strands, respectively). The dCTP base is seen in a
stacking arrangement with the 3â end base of the primer strand,
suggesting that this complex is functionally relevant. (Figure
continues on facing page.)
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Figure 3.
Fig. 3. Distances bwteen the nucleotides and interacting protein side chains.
Only potential H-bonds are shown. A: Klentaql with dATP.
B: Klentaql with dCTP. C: Klentaql with dGTP. D: Klentaql with dTTP.
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The above figures are
reprinted
from an Open Access publication published by the Protein Society:
Protein Sci
(1998,
7,
1116-1123)
copyright 1998.
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