5vu8: Difference between revisions
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==TNA polymerase, closed ternary complex== | ==TNA polymerase, closed ternary complex== | ||
<StructureSection load='5vu8' size='340' side='right' caption='[[5vu8]], [[Resolution|resolution]] 3.20Å' scene=''> | <StructureSection load='5vu8' size='340' side='right'caption='[[5vu8]], [[Resolution|resolution]] 3.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5vu8]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU8 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5vu8]] 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=5VU8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VU8 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=9O7:[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl]+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>9O7</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.2Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=9O4:[(3~{R},5~{R})-5-(6-aminopurin-9-yl)oxolan-3-yl]+dihydrogen+phosphate'>9O4</scene>, <scene name='pdbligand=9O7:[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl]+[oxidanyl(phosphonooxy)phosphoryl]+hydrogen+phosphate'>9O7</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5vu8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu8 OCA], [https://pdbe.org/5vu8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vu8 RCSB], [https://www.ebi.ac.uk/pdbsum/5vu8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu8 ProSAT]</span></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 5vu8" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[DNA polymerase 3D structures|DNA polymerase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: Synthetic construct]] | ||
[[Category: | [[Category: Thermococcus kodakarensis]] | ||
[[Category: | [[Category: Chaput JC]] | ||
[[Category: | [[Category: Chim N]] | ||
Latest revision as of 15:16, 6 November 2024
TNA polymerase, closed ternary complexTNA polymerase, closed ternary complex
Structural highlights
FunctionPublication Abstract from PubMedDarwinian 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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