3pv8: Difference between revisions
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<StructureSection load='3pv8' size='340' side='right' caption='[[3pv8]], [[Resolution|resolution]] 1.52Å' scene=''> | <StructureSection load='3pv8' size='340' side='right' caption='[[3pv8]], [[Resolution|resolution]] 1.52Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3pv8]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PV8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PV8 FirstGlance]. <br> | <table><tr><td colspan='2'>[[3pv8]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_kaustophilus"_prickett_1928 "bacillus kaustophilus" prickett 1928]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PV8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PV8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D3T:2,3-DIDEOXY-THYMIDINE-5-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=D3T:2,3-DIDEOXY-THYMIDINE-5-TRIPHOSPHATE'>D3T</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DT:3-DEOXYTHYMIDINE-5-MONOPHOSPHATE'>2DT</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3px0|3px0]], [[3px4|3px4]], [[3px6|3px6]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3px0|3px0]], [[3px4|3px4]], [[3px6|3px6]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polA, GK2730 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1462 "Bacillus kaustophilus" Prickett 1928])</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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pv8 OCA], [http://pdbe.org/3pv8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pv8 RCSB], [http://www.ebi.ac.uk/pdbsum/3pv8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pv8 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3pv8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pv8 OCA], [http://pdbe.org/3pv8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pv8 RCSB], [http://www.ebi.ac.uk/pdbsum/3pv8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pv8 ProSAT]</span></td></tr> | ||
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</div> | </div> | ||
<div class="pdbe-citations 3pv8" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 3pv8" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus kaustophilus prickett 1928]] | |||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Beese, L S]] | [[Category: Beese, L S]] | ||
Revision as of 13:59, 13 February 2019
Crystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed ConformationCrystal Structure of Bacillus DNA Polymerase I Large Fragment Bound to DNA and ddTTP-dA in Closed Conformation
Structural highlights
Publication Abstract from PubMedEven though high-fidelity polymerases copy DNA with remarkable accuracy, some base-pair mismatches are incorporated at low frequency, leading to spontaneous mutagenesis. Using high-resolution X-ray crystallographic analysis of a DNA polymerase that catalyzes replication in crystals, we observe that a C*A mismatch can mimic the shape of cognate base pairs at the site of incorporation. This shape mimicry enables the mismatch to evade the error detection mechanisms of the polymerase, which would normally either prevent mismatch incorporation or promote its nucleolytic excision. Movement of a single proton on one of the mismatched bases alters the hydrogen-bonding pattern such that a base pair forms with an overall shape that is virtually indistinguishable from a canonical, Watson-Crick base pair in double-stranded DNA. These observations provide structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis, a long-standing concept that has been difficult to demonstrate directly. Structural evidence for the rare tautomer hypothesis of spontaneous mutagenesis.,Wang W, Hellinga HW, Beese LS Proc Natl Acad Sci U S A. 2011 Oct 25;108(43):17644-8. Epub 2011 Oct 17. PMID:22006298[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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