2asd
From Proteopedia
(New page: 200px<br /><applet load="2asd" size="450" color="white" frame="true" align="right" spinBox="true" caption="2asd, resolution 1.95Å" /> '''oxoG-modified Insert...) |
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| - | [[Image:2asd.gif|left|200px]]<br /><applet load="2asd" size=" | + | [[Image:2asd.gif|left|200px]]<br /><applet load="2asd" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2asd, resolution 1.95Å" /> | caption="2asd, resolution 1.95Å" /> | ||
'''oxoG-modified Insertion Ternary Complex'''<br /> | '''oxoG-modified Insertion Ternary 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== | ||
| - | 2ASD 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 and DCP 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:// | + | 2ASD 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> and <scene name='pdbligand=DCP:'>DCP</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=2ASD 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 16:30:29 2008'' |
Revision as of 14:30, 21 February 2008
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oxoG-modified Insertion Ternary Complex
Overview
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
2ASD is a Single protein structure of sequence from Sulfolobus solfataricus with and as ligands. Active as DNA-directed DNA polymerase, with EC number 2.7.7.7 Full crystallographic information is available from OCA.
Reference
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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