5yte: Difference between revisions

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-'''Unreleased structure'''
-The entry 5yte is ON HOLD  until Paper Publication
+==Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair==
+<StructureSection load='5yte' size='340' side='right' caption='[[5yte]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5yte]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25104 Atcc 25104]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YTE FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">polA, pol1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=271 ATCC 25104])</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=5yte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yte OCA], [http://pdbe.org/5yte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yte RCSB], [http://www.ebi.ac.uk/pdbsum/5yte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yte ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which DNA polymerases faithfully decode chemical information on the template. It was previously shown that two unnatural cytosine bases (termed "M-fC" and "I-fC"), which are chemical labeling adducts of the epigenetic base 5-formylcytosine, can induce C-to-T transition during DNA amplification. However, how DNA polymerases recognize such unnatural cytosine bases remains enigmatic. Herein, crystal structures of unnatural cytosine bases pairing to dA/dG in the KlenTaq polymerase-host-guest complex system and pairing to dATP in the KlenTaq polymerase active site were determined. Both M-fC and I-fC base pair with dA/dATP, but not with dG, in a Watson-Crick geometry. This study reveals that the formation of the Watson-Crick geometry, which may be enabled by the A-rule, is important for the recognition of unnatural cytosines.
-Authors: Zeng, H., Mondal, M., Song, R.Y., Zhang, J., Xia, B., Gao, Y.Q., Yi, C.Q.
+Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.,Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao YQ, Yi C Angew Chem Int Ed Engl. 2019 Jan 2;58(1):130-133. doi: 10.1002/anie.201807845., Epub 2018 Dec 5. PMID:30407705<ref>PMID:30407705</ref>
-Description: Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with with natural dT:dATP base pair
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Song, R.Y]]
+<div class="pdbe-citations 5yte" style="background-color:#fffaf0;"></div>
-[[Category: Yi, C.Q]]
+== References ==
-[[Category: Gao, Y.Q]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Atcc 25104]]
+[[Category: DNA-directed DNA polymerase]]
+[[Category: Gao, Y Q]]
+[[Category: Mondal, M]]
+[[Category: Song, R Y]]
 [[Category: Xia, B]]
+[[Category: Yi, C Q]]
+[[Category: Zeng, H]]
 [[Category: Zhang, J]]
-[[Category: Zeng, H]]
+[[Category: Replication-dna complex]]
-[[Category: Mondal, M]]