5vu9: Difference between revisions

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 ==TNA polymerase, translocated product==
-<StructureSection load='5vu9' size='340' side='right' caption='[[5vu9]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='5vu9' size='340' side='right'caption='[[5vu9]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5vu9]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VU9 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5vu9]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis Thermococcus kodakarensis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VU9 FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vu5|5vu5]], [[5vu6|5vu6]], [[5vu7|5vu7]], [[5vu8|5vu8]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FA2:5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXYTETRAHYDROFURAN-3-YL+DIHYDROGEN+PHOSPHATE'>FA2</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=5vu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu9 OCA], [https://pdbe.org/5vu9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vu9 RCSB], [https://www.ebi.ac.uk/pdbsum/5vu9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu9 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=5vu9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu9 OCA], [http://pdbe.org/5vu9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu9 ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/D0VWU9_THEKO D0VWU9_THEKO]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Darwinian evolution experiments carried out on xeno-nucleic acid (XNA) polymers require engineered polymerases that can faithfully and efficiently copy genetic information back and forth between DNA and XNA. However, current XNA polymerases function with inferior activity relative to their natural counterparts. Here, we report five X-ray crystal structures that illustrate the pathway by which alpha-(L)-threofuranosyl nucleic acid (TNA) triphosphates are selected and extended in a template-dependent manner using a laboratory-evolved polymerase known as Kod-RI. Structural comparison of the apo, binary, open and closed ternary, and translocated product detail an ensemble of interactions and conformational changes required to promote TNA synthesis. Close inspection of the active site in the closed ternary structure reveals a sub-optimal binding geometry that explains the slow rate of catalysis. This key piece of information, which is missing for all naturally occurring archaeal DNA polymerases, provides a framework for engineering new TNA polymerase variants.
+Structural basis for TNA synthesis by an engineered TNA polymerase.,Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC Nat Commun. 2017 Nov 27;8(1):1810. doi: 10.1038/s41467-017-02014-0. PMID:29180809<ref>PMID:29180809</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5vu9" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[DNA polymerase 3D structures|DNA polymerase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: DNA-directed DNA polymerase]]
+[[Category: Large Structures]]
-[[Category: Chaput, J C]]
+[[Category: Synthetic construct]]
-[[Category: Chim, N]]
+[[Category: Thermococcus kodakarensis]]
-[[Category: Protein-nucleic acid complex]]
+[[Category: Chaput JC]]
-[[Category: Transferase-dna complex]]
+[[Category: Chim N]]