5vu9: Difference between revisions

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<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 ==
== 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 [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=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>
</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='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>
<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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5vu5|5vu5]], [[5vu6|5vu6]], [[5vu7|5vu7]], [[5vu8|5vu8]]</td></tr>
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<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>
<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>
</table>
<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>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Thermococcus kodakaraensis atomi et al. 2004]]
[[Category: DNA-directed DNA polymerase]]
[[Category: DNA-directed DNA polymerase]]
[[Category: Chaput, J C]]
[[Category: Chaput, J C]]

Revision as of 10:33, 13 December 2017

TNA polymerase, translocated productTNA polymerase, translocated product

Structural highlights

5vu9 is a 3 chain structure with sequence from "thermococcus_kodakaraensis"_atomi_et_al._2004 "thermococcus kodakaraensis" atomi et al. 2004. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Activity:DNA-directed DNA polymerase, with EC number 2.7.7.7
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

References

  1. ↑ 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

5vu9, resolution 2.05Å

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