2xo7: Difference between revisions
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==CRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS== | ==CRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS== | ||
<StructureSection load='2xo7' size='340' side='right' caption='[[2xo7]], [[Resolution|resolution]] 2.85Å' scene=''> | <StructureSection load='2xo7' size='340' side='right' caption='[[2xo7]], [[Resolution|resolution]] 2.85Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2xo7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[2xo7]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_12980 Atcc 12980]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XO7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XO7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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=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=47C:2-DEOXY-N-(PROP-2-EN-1-YLOXY)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>47C</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=47C:2-DEOXY-N-(PROP-2-EN-1-YLOXY)CYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>47C</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xo9|2xo9]], [[2xoh|2xoh]], [[2xoj|2xoj]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2xo9|2xo9]], [[2xoh|2xoh]], [[2xoj|2xoj]]</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=2xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xo7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2xo7 RCSB], [http://www.ebi.ac.uk/pdbsum/2xo7 PDBsum]</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=2xo7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xo7 OCA], [http://pdbe.org/2xo7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xo7 RCSB], [http://www.ebi.ac.uk/pdbsum/2xo7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xo7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
</jmolCheckbox> | </jmolCheckbox> | ||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/ | </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2xo7 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | </div> | ||
<div class="pdbe-citations 2xo7" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Atcc 12980]] | |||
[[Category: DNA-directed DNA polymerase]] | [[Category: DNA-directed DNA polymerase]] | ||
[[Category: Carell, T]] | [[Category: Carell, T]] | ||
[[Category: Lercher, L]] | [[Category: Lercher, L]] | ||
Revision as of 18:10, 11 August 2016
CRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUSCRYSTAL STRUCTURE OF A DA:O-ALLYLHYDROXYLAMINE-DC BASEPAIR IN COMPLEX WITH FRAGMENT DNA POLYMERASE I FROM BACILLUS STEAROTHERMOPHILUS
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 PubMedThe presence of the methylated nucleobase (5Me)dC in CpG islands is a key factor that determines gene silencing. False methylation patterns are responsible for deteriorated cellular development and are a hallmark of many cancers. Today genes can be sequenced for the content of (5Me)dC only with the help of the bisulfite reagent, which is based exclusively on chemical reactivity differences established by the additional methyl group. Despite intensive optimization of the bisulfite protocol, the method still has specificity problems. Most importantly approximately 95% of the DNA analyte is degraded during the analysis procedure. We discovered that the reagent O-allylhydroxylamine is able to discriminate between dC and (5Me)dC. The reagent, in contrast to bisulfite, does not exploit reactivity differences but gives directly different reaction products. The reagent forms a stable mutagenic adduct with dC, which can exist in two states (E versus Z). In case of dC the allylhydroxylamine adduct switches into the E-isomeric form, which generates dC to dT transition mutations that can easily be detected by established methods. Significantly, the (5Me)dC-adduct adopts exclusively the Z-isomeric form, which causes the polymerase to stop. O-allylhydroxylamine does allow differentiation between dC and (5Me)dC with high accuracy, leading towards a novel and mild chemistry for methylation analysis. Chemical discrimination between dC and 5MedC via their hydroxylamine adducts.,Munzel M, Lercher L, Muller M, Carell T Nucleic Acids Res. 2010 Sep 2. PMID:20813757[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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