2atl: Difference between revisions
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|PDB= 2atl |SIZE=350|CAPTION= <scene name='initialview01'>2atl</scene>, resolution 2.80Å | |PDB= 2atl |SIZE=350|CAPTION= <scene name='initialview01'>2atl</scene>, resolution 2.80Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene> | |LIGAND= <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DCP:2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE'>DCP</scene>, <scene name='pdbligand=DDG:2',3'-DIDEOXY-GUANOSINE-5'-MONOPHOSPHATE'>DDG</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> | ||
|ACTIVITY= [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] | |ACTIVITY= <span class='plainlinks'>[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] </span> | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY=[[2asd|2ASD]], [[2asj|2ASJ]], [[2asl|2ASL]] | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2atl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2atl OCA], [http://www.ebi.ac.uk/pdbsum/2atl PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2atl RCSB]</span> | |||
}} | }} | ||
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[[Category: Patel, D J.]] | [[Category: Patel, D J.]] | ||
[[Category: Rechkoblit, O.]] | [[Category: Rechkoblit, O.]] | ||
[[Category: dna polymerase]] | [[Category: dna polymerase]] | ||
[[Category: lesion bypass]] | [[Category: lesion bypass]] | ||
[[Category: y-family]] | [[Category: y-family]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:57:08 2008'' | ||
Revision as of 01:57, 31 March 2008
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| , resolution 2.80Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Activity: | DNA-directed DNA polymerase, with EC number 2.7.7.7 | ||||||
| Related: | 2ASD, 2ASJ, 2ASL
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Unmodified Insertion Ternary 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
2ATL is a Single protein structure of sequence from Sulfolobus solfataricus. 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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