3ski: Difference between revisions
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==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine== | ==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine== | ||
<StructureSection load='3ski' size='340' side='right' caption='[[3ski]], [[Resolution|resolution]] 2.30Å' scene=''> | <StructureSection load='3ski' size='340' side='right'caption='[[3ski]], [[Resolution|resolution]] 2.30Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ski]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKI OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[3ski]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SKI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SKI FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | ||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr> | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3skz|3skz]], [[3slq|3slq]], [[3slm|3slm]], [[3skl|3skl]], [[3skw|3skw]], [[3skt|3skt]], [[3skr|3skr]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3skz|3skz]], [[3slq|3slq]], [[3slm|3slm]], [[3skl|3skl]], [[3skw|3skw]], [[3skt|3skt]], [[3skr|3skr]]</div></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ski FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ski OCA], [https://pdbe.org/3ski PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ski RCSB], [https://www.ebi.ac.uk/pdbsum/3ski PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ski ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Patel, D J]] | [[Category: Patel, D J]] | ||
[[Category: Pikovskaya, O]] | [[Category: Pikovskaya, O]] | ||
Revision as of 10:59, 29 June 2022
Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosineCrystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine
Structural highlights
Publication Abstract from PubMedPurine riboswitches have an essential role in genetic regulation of bacterial metabolism. This family includes the 2'-deoxyguanosine (dG) riboswitch, which is involved in feedback control of deoxyguanosine biosynthesis. To understand the principles that define dG selectivity, we determined crystal structures of the natural Mesoplasma florum riboswitch bound to cognate dG as well as to noncognate guanosine, deoxyguanosine monophosphate and guanosine monophosphate. Comparison with related purine riboswitch structures reveals that the dG riboswitch achieves its specificity through modification of key interactions involving the nucleobase and rearrangement of the ligand-binding pocket to accommodate the additional sugar moiety. In addition, we observe new conformational changes beyond the junctional binding pocket extending as far as peripheral loop-loop interactions. It appears that re-engineering riboswitch scaffolds will require consideration of selectivity features dispersed throughout the riboswitch tertiary fold, and structure-guided drug design efforts targeted to junctional RNA scaffolds need to be addressed within such an expanded framework. Structural principles of nucleoside selectivity in a 2'-deoxyguanosine riboswitch.,Pikovskaya O, Polonskaia A, Patel DJ, Serganov A Nat Chem Biol. 2011 Aug 14;7(10):748-55. doi: 10.1038/nchembio.631. PMID:21841796[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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