1tk8: Difference between revisions
New page: left|200px<br /><applet load="1tk8" size="450" color="white" frame="true" align="right" spinBox="true" caption="1tk8, resolution 2.50Å" /> '''T7 DNA polymerase te... |
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[[Image:1tk8.gif|left|200px]]<br /><applet load="1tk8" size=" | [[Image:1tk8.gif|left|200px]]<br /><applet load="1tk8" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1tk8, resolution 2.50Å" /> | caption="1tk8, resolution 2.50Å" /> | ||
'''T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site'''<br /> | '''T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site'''<br /> | ||
==Overview== | ==Overview== | ||
Accurate DNA replication involves polymerases with high nucleotide | Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG. | ||
==About this Structure== | ==About this Structure== | ||
1TK8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG, SO4, D3T, MES and 1PE as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http:// | 1TK8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bacteriophage_t7 Bacteriophage t7] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=D3T:'>D3T</scene>, <scene name='pdbligand=MES:'>MES</scene> and <scene name='pdbligand=1PE:'>1PE</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/DNA-directed_DNA_polymerase DNA-directed DNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.7 2.7.7.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TK8 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Brieba, L | [[Category: Brieba, L G.]] | ||
[[Category: Doublie, S.]] | [[Category: Doublie, S.]] | ||
[[Category: Eichman, B | [[Category: Eichman, B F.]] | ||
[[Category: Ellenberger, T.]] | [[Category: Ellenberger, T.]] | ||
[[Category: Kokoska, R | [[Category: Kokoska, R J.]] | ||
[[Category: Kunkel, T | [[Category: Kunkel, T A.]] | ||
[[Category: 1PE]] | [[Category: 1PE]] | ||
[[Category: D3T]] | [[Category: D3T]] | ||
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[[Category: 8-oxoguanosine dna polymerase]] | [[Category: 8-oxoguanosine dna polymerase]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:14:23 2008'' | ||
Revision as of 16:14, 21 February 2008
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T7 DNA polymerase ternary complex with 8 oxo guanosine and dAMP at the elongation site
OverviewOverview
Accurate DNA replication involves polymerases with high nucleotide selectivity and proofreading activity. We show here why both fidelity mechanisms fail when normally accurate T7 DNA polymerase bypasses the common oxidative lesion 8-oxo-7, 8-dihydro-2'-deoxyguanosine (8oG). The crystal structure of the polymerase with 8oG templating dC insertion shows that the O8 oxygen is tolerated by strong kinking of the DNA template. A model of a corresponding structure with dATP predicts steric and electrostatic clashes that would reduce but not eliminate insertion of dA. The structure of a postinsertional complex shows 8oG(syn).dA (anti) in a Hoogsteen-like base pair at the 3' terminus, and polymerase interactions with the minor groove surface of the mismatch that mimic those with undamaged, matched base pairs. This explains why translesion synthesis is permitted without proofreading of an 8oG.dA mismatch, thus providing insight into the high mutagenic potential of 8oG.
About this StructureAbout this Structure
1TK8 is a Protein complex structure of sequences from Bacteriophage t7 and Escherichia coli with , , , and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase., Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, Ellenberger T, EMBO J. 2004 Sep 1;23(17):3452-61. Epub 2004 Aug 5. PMID:15297882
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