2j6t: Difference between revisions
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==Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.== | ==Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.== | ||
<StructureSection load='2j6t' size='340' side='right' caption='[[2j6t]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='2j6t' size='340' side='right'caption='[[2j6t]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2j6t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J6T OCA]. For a <b>guided tour on the structure components</b> use [http:// | <table><tr><td colspan='2'>[[2j6t]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2J6T OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2J6T FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6OG:6-O-METHYL+GUANOSINE-5-MONOPHOSPHATE'>6OG</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jx4|1jx4]], [[1jxl|1jxl]], [[1n48|1n48]], [[1n56|1n56]], [[1ryr|1ryr]], [[1rys|1rys]], [[1s0m|1s0m]], [[1s0n|1s0n]], [[1s0o|1s0o]], [[1s10|1s10]], [[1s97|1s97]], [[1s9f|1s9f]], [[2ago|2ago]], [[2agp|2agp]], [[2agq|2agq]], [[2asd|2asd]], [[2asj|2asj]], [[2asl|2asl]], [[2atl|2atl]], [[2au0|2au0]], [[2bq3|2bq3]], [[2bqr|2bqr]], [[2bqu|2bqu]], [[2br0|2br0]], [[2c22|2c22]], [[2c28|2c28]], [[2c2d|2c2d]], [[2c2e|2c2e]], [[2c2r|2c2r]], [[2j6s|2j6s]], [[2j6u|2j6u]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1jx4|1jx4]], [[1jxl|1jxl]], [[1n48|1n48]], [[1n56|1n56]], [[1ryr|1ryr]], [[1rys|1rys]], [[1s0m|1s0m]], [[1s0n|1s0n]], [[1s0o|1s0o]], [[1s10|1s10]], [[1s97|1s97]], [[1s9f|1s9f]], [[2ago|2ago]], [[2agp|2agp]], [[2agq|2agq]], [[2asd|2asd]], [[2asj|2asj]], [[2asl|2asl]], [[2atl|2atl]], [[2au0|2au0]], [[2bq3|2bq3]], [[2bqr|2bqr]], [[2bqu|2bqu]], [[2br0|2br0]], [[2c22|2c22]], [[2c28|2c28]], [[2c2d|2c2d]], [[2c2e|2c2e]], [[2c2r|2c2r]], [[2j6s|2j6s]], [[2j6u|2j6u]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http:// | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2j6t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2j6t OCA], [http://pdbe.org/2j6t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2j6t RCSB], [http://www.ebi.ac.uk/pdbsum/2j6t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2j6t ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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==See Also== | ==See Also== | ||
*[[DNA polymerase|DNA polymerase]] | *[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
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</StructureSection> | </StructureSection> | ||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Large Structures]] | |||
[[Category: Sulso]] | [[Category: Sulso]] | ||
[[Category: Egli, M]] | [[Category: Egli, M]] | ||
Revision as of 10:42, 15 April 2020
Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.Ternary complex of Sulfolobus solfataricus Dpo4 DNA polymerase, O6- methylguanine modified DNA, and dATP.
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedWe examined the effect of a single O6-methylguanine (O6-MeG) template residue on catalysis by a model Y family polymerase, Dpo4 from Sulfolobus solfataricus. Mass spectral analysis of Dpo4-catalyzed extension products revealed that the enzyme accurately bypasses O6-MeG, with C being the major product (approximately 70%) and T or A being the minor species (approximately 20% or approximately 10%, respectively), consistent with steady-state kinetic parameters. Transient-state kinetic experiments revealed that kpol, the maximum forward rate constant describing polymerization, for dCTP incorporation opposite O6-MeG was approximately 6-fold slower than observed for unmodified G, and no measurable product was observed for dTTP incorporation in the pre-steady state. The lack of any structural information regarding how O6-MeG paired in a polymerase active site led us to perform x-ray crystallographic studies, which show that "wobble" pairing occurs between C and O6-MeG. A structure containing T opposite O6-MeG was solved, but much of the ribose and pyrimidine base density was disordered, in accordance with a much higher Km,dTTP that drives the difference in efficiency between C and T incorporation. The more stabilized C:O6-MeG pairing reinforces the importance of hydrogen bonding with respect to nucleotide selection within a geometrically tolerant polymerase active site. Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred.,Eoff RL, Irimia A, Egli M, Guengerich FP J Biol Chem. 2007 Jan 12;282(2):1456-67. Epub 2006 Nov 14. PMID:17105728[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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