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PDBsum entry 1zqo
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Transferase/DNA
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PDB id
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1zqo
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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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Characterization of the metal ion binding helix-Hairpin-Helix motifs in human DNA polymerase beta by x-Ray structural analysis.
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Authors
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H.Pelletier,
M.R.Sawaya.
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Ref.
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Biochemistry, 1996,
35,
12778-12787.
[DOI no: ]
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PubMed id
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Abstract
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X-ray crystallographic studies have shown that DNA binding by human polymerase
beta (pol beta) occurs primarily through two structurally and sequentially
homologous helix-hairpin-helix (HhH) motifs, one in the fingers subdomain and
the other in the 8-kDa domain [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson,
S. H., & Kraut, J. (1996a) Biochemistry 35, 12742-12761]. In that DNA
binding by each HhH motif is facilitated by a metal ion, we set out to determine
the identity of the metal ion that most likely binds to the HhH motif in vivo.
Crystal soaking experiments were performed on human pol beta-DNA cocrystals with
Mg2+, Ca2+, Na+, and K+, the four most prevalent metal ions in the cell, and in
each case a data set was collected and the resulting structure was refined.
Under the conditions tested, the HhH motifs of pol beta have an affinity for
these biologically prevalent metal ions in the order Mg2+ < Ca2+ < Na+
< K+, with K+ displaying the strongest binding. Crystals soaked in the
presence of Tl+, a commonly used spectroscopic probe for K+, were too
X-ray-sensitive to establish the binding behavior of Tl+, but soaking
experiments with Ba2+ and Cs+ resulted in relatively stable crystals that gave
evidence of metal ion binding in both HhH motifs, confirming that larger
monovalent and divalent metal ions are capable of binding to the HhH metal
sites. Although Mn2+, which has been categorized as a potent polymerase mutagen,
binds to the HhH motifs with a greater affinity than Mg2+, Mn2+ does not bind to
the HhH motifs in the presence of equimolar concentrations of Na+. These results
suggest that in vivo, where Mn2+ is present only in trace amounts, Mn2+ probably
does not have a large effect on DNA binding and may instead manifest a mutagenic
effect on pol beta primarily by distorting nucleotide binding or by directly
affecting the catalytic step [Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson,
S. H., & Kraut, J. (1996b) Biochemistry 35, 12762-12777]. Crystal soaking
experiments with 31-kDa apoenzyme crystals show that, in the absence of DNA, the
HhH motif in the fingers subdomain binds metal ions with either much lower
occupancy or not at all, indicating that metal ion binding is dependent on the
presence of the DNA substrate.
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Secondary reference #1
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Title
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Crystal structures of human DNA polymerase beta complexed with nicked and gapped DNA substrates
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Authors
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M.R.Sawaya,
T.Rawson,
S.H.Wilson,
J.Kraut,
H.Pelletier.
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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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The role of thumb movement and template bending in polymerase fidelity
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Author
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H.Pelletier.
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Ref.
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TO BE PUBLISHED ...
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Secondary reference #3
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Title
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Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, Processivity, And fidelity.
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Authors
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H.Pelletier,
M.R.Sawaya,
W.Wolfle,
S.H.Wilson,
J.Kraut.
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Ref.
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Biochemistry, 1996,
35,
12742-12761.
[DOI no: ]
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PubMed id
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Secondary reference #4
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Title
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A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
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Authors
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H.Pelletier,
M.R.Sawaya,
W.Wolfle,
S.H.Wilson,
J.Kraut.
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Ref.
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Biochemistry, 1996,
35,
12762-12777.
[DOI no: ]
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PubMed id
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Secondary reference #5
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Title
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Characterization of the metal ion binding helix-Hairpin-Helix motifs in human DNA polymerase beta by x-Ray structural analysis.
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Authors
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H.Pelletier,
M.R.Sawaya.
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Ref.
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Biochemistry, 1996,
35,
12778-12787.
[DOI no: ]
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PubMed id
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Secondary reference #6
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Title
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Polymerase structures and mechanism.
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Author
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H.Pelletier.
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Ref.
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Science, 1994,
266,
2025-2026.
[DOI no: ]
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PubMed id
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Secondary reference #7
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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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Secondary reference #8
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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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