View source for 6txr


==Structural insights into cubane-modified aptamer recognition of a malaria biomarker==
<StructureSection load='6txr' size='340' side='right'caption='[[6txr]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6txr]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TXR FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene>, <scene name='pdbligand=O0Q:~{N}-[2-(1,2,3-triazol-1-yl)ethyl]cubane-1-carboxamide'>O0Q</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=6txr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6txr OCA], [https://pdbe.org/6txr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6txr RCSB], [https://www.ebi.ac.uk/pdbsum/6txr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6txr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q4PRK9_PLAVI Q4PRK9_PLAVI] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker Plasmodium vivax lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of P. vivax over Plasmodium falciparum lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.

Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker.,Cheung YW, Rothlisberger P, Mechaly AE, Weber P, Levi-Acobas F, Lo Y, Wong AWC, Kinghorn AB, Haouz A, Savage GP, Hollenstein M, Tanner JA Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):16790-16798. doi:, 10.1073/pnas.2003267117. Epub 2020 Jul 6. PMID:32631977<ref>PMID:32631977</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6txr" style="background-color:#fffaf0;"></div>

==See Also==
*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Plasmodium vivax]]
[[Category: Cheung Y]]
[[Category: Haouz A]]
[[Category: Hollenstein M]]
[[Category: Lo Y]]
[[Category: Mechaly A]]
[[Category: Roethlisberger P]]
[[Category: Savage P]]
[[Category: Tanner J]]
[[Category: Weber P]]
[[Category: Wong A]]