5hru: Difference between revisions
New page: '''Unreleased structure''' The entry 5hru is ON HOLD Authors: Choi, S.J., Ban, C. Description: Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1 [[Cate... |
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==Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1== | |||
<StructureSection load='5hru' size='340' side='right'caption='[[5hru]], [[Resolution|resolution]] 1.71Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5hru]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Phylica_emirnensis Phylica emirnensis] and [https://en.wikipedia.org/wiki/Plasmodium_vivax Plasmodium vivax]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5HRU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HRU 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]] 1.71Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=5hru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hru OCA], [https://pdbe.org/5hru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hru RCSB], [https://www.ebi.ac.uk/pdbsum/5hru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hru ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q4PRK9_PLAVI Q4PRK9_PLAVI] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Structural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G.G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s. | |||
Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.,Choi SJ, Ban C Sci Rep. 2016 Oct 11;6:34998. doi: 10.1038/srep34998. PMID:27725738<ref>PMID:27725738</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5hru" style="background-color:#fffaf0;"></div> | ||
[[Category: Ban | |||
==See Also== | |||
*[[Lactate dehydrogenase 3D structures|Lactate dehydrogenase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Phylica emirnensis]] | |||
[[Category: Plasmodium vivax]] | |||
[[Category: Ban C]] | |||
[[Category: Choi SJ]] | |||
Latest revision as of 13:52, 16 August 2023
Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1Crystal structure of Plasmodium vivax LDH in complex with a DNA aptamer called pL1
Structural highlights
FunctionPublication Abstract from PubMedStructural elements are key elements for understanding single-stranded nucleic acid folding. Although various RNA structural elements have been documented, structural elements of single-stranded DNA (ssDNA) have rarely been reported. Herein, we determined a crystal structure of PvLDH in complex with a DNA aptamer called pL1. This aptamer folds into a hairpin-bulge contact by adopting three novel structural elements, viz, DNA T-loop-like motif, base-phosphate zipper, and DNA G.G metal ion zipper. Moreover, the pL1:PvLDH complex shows unique properties compared with other protein:nucleic acid complexes. Generally, extensive intermolecular hydrogen bonds occur between unpaired nucleotides and proteins for specific recognitions. Although most protein-interacting nucleotides of pL1 are unpaired nucleotides, pL1 recognizes PvLDH by predominant shape complementarity with many bridging water molecules owing to the combination of three novel structural elements making protein-binding unpaired nucleotides stable. Moreover, the additional set of Plasmodium LDH residues which were shown to form extensive hydrogen bonds with unpaired nucleotides of 2008s does not participate in the recognition of pL1. Superimposition of the pL1:PvLDH complex with hLDH reveals steric clashes between pL1 and hLDH in contrast with no steric clashes between 2008s and hLDH. Therefore, specific protein recognition mode of pL1 is totally different from that of 2008s. Crystal structure of a DNA aptamer bound to PvLDH elucidates novel single-stranded DNA structural elements for folding and recognition.,Choi SJ, Ban C Sci Rep. 2016 Oct 11;6:34998. doi: 10.1038/srep34998. PMID:27725738[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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