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PDBsum entry 2bpf
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Transferase/DNA
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PDB id
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2bpf
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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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Structures of ternary complexes of rat DNA polymerase beta, A DNA template-Primer, And ddctp.
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Authors
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H.Pelletier,
M.R.Sawaya,
A.Kumar,
S.H.Wilson,
J.Kraut.
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Ref.
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Science, 1994,
264,
1891-1903.
[DOI no: ]
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PubMed id
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Abstract
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Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA
template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined
at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of
dideoxycytidine (ddC), a nucleoside analog that targets the reverse
transcriptase of human immunodeficiency virus (HIV) and is at present used to
treat AIDS. Although crystals of the two complexes belong to different space
groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP
interactions are not affected by crystal packing forces. In the pol beta active
site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and
two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these
residues, Asp190 and Asp256, are present in the amino acid sequences of all
polymerases so far studied and are also spatially similar in the four
polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1
reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal
structures are now known. A two-metal ion mechanism is described for the
nucleotidyl transfer reaction and may apply to all polymerases. In the ternary
complex structures analyzed, pol beta binds to the DNA template-primer in a
different manner from that recently proposed for other polymerase-DNA models.
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Secondary reference #1
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Title
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Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
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Authors
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M.R.Sawaya,
H.Pelletier,
A.Kumar,
S.H.Wilson,
J.Kraut.
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Ref.
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Science, 1994,
264,
1930-1935.
[DOI no: ]
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PubMed id
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