2au0: Difference between revisions
New page: left|200px<br /><applet load="2au0" size="450" color="white" frame="true" align="right" spinBox="true" caption="2au0, resolution 2.70Å" /> '''Unmodified preinsert... |
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[[Image:2au0.gif|left|200px]]<br /><applet load="2au0" size=" | [[Image:2au0.gif|left|200px]]<br /><applet load="2au0" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="2au0, resolution 2.70Å" /> | caption="2au0, resolution 2.70Å" /> | ||
'''Unmodified preinsertion binary complex'''<br /> | '''Unmodified preinsertion binary complex'''<br /> | ||
==Overview== | ==Overview== | ||
7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following | 7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG*C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases. | ||
==About this Structure== | ==About this Structure== | ||
2AU0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with CA as [http://en.wikipedia.org/wiki/ligand ligand]. 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:// | 2AU0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus Sulfolobus solfataricus] with <scene name='pdbligand=CA:'>CA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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=2AU0 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Broyde, S.]] | [[Category: Broyde, S.]] | ||
[[Category: Cheng, Y.]] | [[Category: Cheng, Y.]] | ||
[[Category: Geacintov, N | [[Category: Geacintov, N E.]] | ||
[[Category: Kuryavyi, V.]] | [[Category: Kuryavyi, V.]] | ||
[[Category: Malinina, L.]] | [[Category: Malinina, L.]] | ||
[[Category: Patel, D | [[Category: Patel, D J.]] | ||
[[Category: Rechkoblit, O.]] | [[Category: Rechkoblit, O.]] | ||
[[Category: CA]] | [[Category: CA]] | ||
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[[Category: y-family]] | [[Category: y-family]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:30:58 2008'' | ||
Revision as of 17:30, 21 February 2008
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Unmodified preinsertion binary complex
OverviewOverview
7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG*C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases.
About this StructureAbout this Structure
2AU0 is a Single protein structure of sequence from Sulfolobus solfataricus with as ligand. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
ReferenceReference
Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion., Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, Geacintov NE, Patel DJ, PLoS Biol. 2006 Jan;4(1):e11. PMID:16379496
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