7u0y
From Proteopedia
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<table><tr><td colspan='2'>[[7u0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0Y FirstGlance]. <br> | <table><tr><td colspan='2'>[[7u0y]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] 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=7U0Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7U0Y 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]] 2.66Å</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]] 2.66Å</td></tr> | ||
| - | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=KY6:4-[(Z)-1-cyano-2- | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=KY6:4-[(~{Z})-1-cyano-2-[6-[2-hydroxyethyl(methyl)amino]-1-benzothiophen-2-yl]ethenyl]benzenecarbonitrile'>KY6</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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y ProSAT]</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=7u0y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7u0y OCA], [https://pdbe.org/7u0y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7u0y RCSB], [https://www.ebi.ac.uk/pdbsum/7u0y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7u0y ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 A resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K(+) dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple.base-triple stack to sandwich the ligand with a U.G wobble pair. Site-bound Mg(2+) ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals. | Pepper is a fluorogenic RNA aptamer tag that binds to a variety of benzylidene-cyanophenyl (HBC) derivatives with tight affinity and activates their fluorescence. To investigate how Pepper RNA folds to create a binding site for HBC, we used antibody-assisted crystallography to determine the structures of Pepper bound to HBC530 and HBC599 to 2.3 and 2.7 A resolutions, respectively. The structural data show that Pepper folds into an elongated structure and organizes nucleotides within an internal bulge to create the ligand binding site, assisted by an out-of-plane platform created by tertiary interactions with an adjacent bulge. As predicted from a lack of K(+) dependence, Pepper does not use a G-quadruplex to form a binding pocket for HBC. Instead, Pepper uses a unique base-quadruple.base-triple stack to sandwich the ligand with a U.G wobble pair. Site-bound Mg(2+) ions support ligand binding structurally and energetically. This research provides insight into the structural features that allow the Pepper aptamer to bind HBC and show how Pepper's function may expand to allow the in vivo detection of other small molecules and metals. | ||
| - | Structural Basis for Fluorescence Activation by Pepper RNA.,Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA ACS Chem Biol. 2022 Jul 15;17(7):1866-1875. doi: 10.1021/acschembio.2c00290. Epub, 2022 Jun 27. PMID:35759696<ref>PMID:35759696</ref> | + | Structural Basis for Fluorescence Activation by Pepper RNA.,Rees HC, Gogacz W, Li NS, Koirala D, Piccirilli JA ACS Chem Biol. 2022 Jul 15;17(7):1866-1875. doi: 10.1021/acschembio.2c00290. Epub , 2022 Jun 27. PMID:35759696<ref>PMID:35759696</ref> |
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
Current revision
Crystal structure of Pepper RNA aptamer in complex with HBC599 ligand and Fab BL3-6
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