7jjf: Difference between revisions

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New page: '''Unreleased structure''' The entry 7jjf is ON HOLD Authors: Harp, J.M., Pallan, P.S., Egli, M. Description: Sarcin-ricin loop with modified residue. [[Category: Unreleased Structures...
 
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'''Unreleased structure'''


The entry 7jjf is ON HOLD
==Sarcin-ricin loop with modified residue.==
<StructureSection load='7jjf' size='340' side='right'caption='[[7jjf]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7jjf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JJF 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]] 1.2&#8491;</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>, <scene name='pdbligand=VC7:5-O-[(R)-hydroxy(methyl)phosphoryl]guanosine'>VC7</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=7jjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jjf OCA], [https://pdbe.org/7jjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jjf RCSB], [https://www.ebi.ac.uk/pdbsum/7jjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jjf ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by GApGA, and the phosphate p stacks on G. We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2...G and Rp-PSO...G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 degrees C in melting temperature Tm and -4.7 kcal/mol in DeltaDeltaG degrees . Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 A longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 A for S vs 1.52 A for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.


Authors: Harp, J.M., Pallan, P.S., Egli, M.
Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.,Pallan PS, Lybrand TP, Schlegel MK, Harp JM, Jahns H, Manoharan M, Egli M Biochemistry. 2020 Dec 15;59(49):4627-4637. doi: 10.1021/acs.biochem.0c00685., Epub 2020 Dec 4. PMID:33275419<ref>PMID:33275419</ref>


Description: Sarcin-ricin loop with modified residue.
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Pallan, P.S]]
<div class="pdbe-citations 7jjf" style="background-color:#fffaf0;"></div>
[[Category: Harp, J.M]]
== References ==
[[Category: Egli, M]]
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Egli M]]
[[Category: Harp JM]]
[[Category: Pallan PS]]
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