 |
PDBsum entry 9icu
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Transferase/DNA
|
PDB id
|
|
|
|
9icu
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
|
|
|
Authors
|
|
H.Pelletier,
M.R.Sawaya,
W.Wolfle,
S.H.Wilson,
J.Kraut.
|
|
|
Ref.
|
|
Biochemistry, 1996,
35,
12762-12777.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
When crystals of human DNA polymerase beta (pol beta) complexed with DNA
[Pelletier, H., Sawaya, M. R., Wolfle, W., Wilson, S. H., & Kraut, J. (1996)
Biochemistry 35, 12742-12761] are soaked in the presence of dATP and Mn2+, X-ray
structural analysis shows that nucleotidyl transfer to the primer 3'-OH takes
place directly in the crystals, even though the DNA is blunt-ended at the active
site. Under similar crystal-soaking conditions, there is no evidence for a
reaction when Mn2+ is replaced by Mg2+, which is thought to be the divalent
metal ion utilized by most polymerases in vivo. These results suggest that one
way Mn2+ may manifest its mutagenic effect on polymerases is by promoting
greater reactivity than Mg2+ at the catalytic site, thereby allowing the
nucleotidyl transfer reaction to take place with little or no regard to
instructions from a template. Non-template-directed nucleotidyl transfer is also
observed when pol beta-DNA cocrystals are soaked in the presence of dATP and
Zn2+, but the reaction products differ in that the sugar moiety of the
incorporated nucleotide appears distorted or otherwise cleaved, in agreement
with reports that Zn2+ may act as a polymerase inhibitor rather than as a
mutagen [Sirover, M. A., & Loeb, L. A. (1976) Science 194, 1434-1436].
Although no reaction is observed when crystals are soaked in the presence of
dATP and other metal ions such as Ca2+, Co2+, Cr3+, or Ni2+, X-ray structural
analyses show that these metal ions coordinate the triphosphate moiety of the
nucleotide in a manner that differs from that observed with Mg2+. In addition,
all metal ions tested, with the exception of Mg2+, promote a change in the
side-chain position of aspartic acid 192, which is one of three highly conserved
active-site carboxylate residues. Soaking experiments with nucleotides other
than dATP (namely, dCTP, dGTP, dTTP, ATP, ddATP, ddCTP, AZT-TP, and dATP alpha
S) reveal a non-base-specific binding site on pol beta for the triphosphate and
sugar moieties of a nucleotide, suggesting a possible mechanism for nucleotide
selectivity whereby triphosphate-sugar binding precedes a check for correct base
pairing with the template.
|
|
|
Secondary reference #1
|
|
|
Title
|
|
Crystal structures of human DNA polymerase beta complexed with nicked and gapped DNA substrates
|
|
|
Authors
|
|
M.R.Sawaya,
T.Rawson,
S.H.Wilson,
J.Kraut,
H.Pelletier.
|
|
|
Ref.
|
|
TO BE PUBLISHED ...
|
|
|
|
Secondary reference #2
|
|
|
Title
|
|
The role of thumb movement and template bending in polymerase fidelity
|
|
|
Author
|
|
H.Pelletier.
|
|
|
Ref.
|
|
TO BE PUBLISHED ...
|
|
|
|
Secondary reference #3
|
|
|
Title
|
|
Crystal structures of human DNA polymerase beta complexed with DNA: implications for catalytic mechanism, Processivity, And fidelity.
|
|
|
Authors
|
|
H.Pelletier,
M.R.Sawaya,
W.Wolfle,
S.H.Wilson,
J.Kraut.
|
|
|
Ref.
|
|
Biochemistry, 1996,
35,
12742-12761.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #4
|
|
|
Title
|
|
A structural basis for metal ion mutagenicity and nucleotide selectivity in human DNA polymerase beta.
|
|
|
Authors
|
|
H.Pelletier,
M.R.Sawaya,
W.Wolfle,
S.H.Wilson,
J.Kraut.
|
|
|
Ref.
|
|
Biochemistry, 1996,
35,
12762-12777.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #5
|
|
|
Title
|
|
Characterization of the metal ion binding helix-Hairpin-Helix motifs in human DNA polymerase beta by x-Ray structural analysis.
|
|
|
Authors
|
|
H.Pelletier,
M.R.Sawaya.
|
|
|
Ref.
|
|
Biochemistry, 1996,
35,
12778-12787.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #6
|
|
|
Title
|
|
Polymerase structures and mechanism.
|
|
|
Author
|
|
H.Pelletier.
|
|
|
Ref.
|
|
Science, 1994,
266,
2025-2026.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #7
|
|
|
Title
|
|
Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
|
|
|
Authors
|
|
M.R.Sawaya,
H.Pelletier,
A.Kumar,
S.H.Wilson,
J.Kraut.
|
|
|
Ref.
|
|
Science, 1994,
264,
1930-1935.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
Secondary reference #8
|
|
|
Title
|
|
Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism.
|
|
|
Authors
|
|
M.R.Sawaya,
H.Pelletier,
A.Kumar,
S.H.Wilson,
J.Kraut.
|
|
|
Ref.
|
|
Science, 1994,
264,
1930-1935.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
|
|
|
|
