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| | <StructureSection load='5vu6' size='340' side='right'caption='[[5vu6]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='5vu6' size='340' side='right'caption='[[5vu6]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5vu6]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VU6 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5vu6]] 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=5VU6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VU6 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]] 3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vu5|5vu5]], [[5vu7|5vu7]], [[5vu8|5vu8]], [[5vu9|5vu9]]</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=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [https://pdbe.org/5vu6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [https://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5vu6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vu6 OCA], [http://pdbe.org/5vu6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vu6 RCSB], [http://www.ebi.ac.uk/pdbsum/5vu6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vu6 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/D0VWU9_THEKO D0VWU9_THEKO] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Thermococcus kodakaraensis atomi et al. 2004]] | |
| - | [[Category: DNA-directed DNA polymerase]] | |
| | [[Category: Large Structures]] | | [[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]] |
| Structural highlights
Function
D0VWU9_THEKO
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Chim N, Shi C, Sau SP, Nikoomanzar A, Chaput JC. Structural basis for TNA synthesis by an engineered TNA polymerase. Nat Commun. 2017 Nov 27;8(1):1810. doi: 10.1038/s41467-017-02014-0. PMID:29180809 doi:http://dx.doi.org/10.1038/s41467-017-02014-0
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