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PDBsum entry 1zet
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Replication/DNA
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PDB id
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1zet
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References listed in PDB file
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Key reference
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Title
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Dna polymerases: hoogsteen base-Pairing in DNA replication?
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Author
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J.Wang.
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Ref.
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Nature, 2005,
437,
E6-7; discussion E7.
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PubMed id
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Abstract
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Human polymerase-iota belongs to the error-prone Y family of polymerases, which
frequently incorporate incorrect nucleotides during DNA replication but can
efficiently bypass DNA lesions. On the basis of X-ray diffraction data, Nair et
al. propose that Hoogsteen base-pairing is adopted by DNA during its replication
by this enzyme. Here I re-examine their X-ray data and find that the electron
density is very weak for a Hoogsteen base pair formed between a template adenine
deoxyribonucleotide in the syn conformation and a deoxythymidine 5'-triphosphate
(dTTP), and that the fit is better for a normal Watson-Crick base pair. As a
guanine-cytosine (G-C) base pair has no potential to form a Hoogsteen base pair
at physiological pH, Hoogsteen base-pairing is unlikely to be used in
replication by this polymerase.
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Secondary reference #1
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Title
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Replication by human DNA polymerase-Iota occurs by hoogsteen base-Pairing.
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Authors
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D.T.Nair,
R.E.Johnson,
S.Prakash,
L.Prakash,
A.K.Aggarwal.
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Ref.
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Nature, 2004,
430,
377-380.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1: Structure of the hPol iota- -DNA
-dTTP ternary complex. The palm, fingers, thumb domains and
the PAD in the two hPol  molecules
are shown in blue, yellow, orange and green, respectively. DNA
is shown in grey and the incoming dTTP in red.
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Figure 2.
Figure 2: Comparison between hPol iota-and
Dpo4. a, Close-up views of the active sites of hPol and
Dpo4. The fingers and palm domains and the PAD are shown in
yellow, blue and green, respectively. The DNA is shown in grey,
and the templating nucleotide and the incoming nucleotide (dTTP
in hPol and
ddADP in Dpo4) in red. The metal ion is dark blue. Highlighted
and labelled are the catalytic residues (Asp 34, Asp 126 and Glu
127 in hPol and
Asp 7, Asp 105 and Glu 106 in Dpo4), the dNTP-bonding residues
(Tyr 39, Tyr 68, Arg 71 and Lys 214 in hPol and
Tyr 12, Tyr 48, Arg 51 and Lys 159 in Dpo4), and the residues
close to the templating base (Gln 59, Lys 60, Leu 62 and Val 64
in hPol and
Val 32, Ala 42 and Ala 44 in Dpo4). Note that the templating
base is in syn conformation in the hPol active
site and in trans conformation in the Dpo4 active site. b,
Close-up views of Hoogsteen base-pairing (dA  dTTP)
in the active site of hPol and
Watson -Crick base-pairing (dT ddADP)
in the active site of Dpo4. c, Close-up views of the nascent
base pair fitting against the hPol and
Dpo4 molecular surfaces. The residues apposed to the templating
base are shown in grey and labelled on the molecular surface.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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