3ski: Difference between revisions

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<StructureSection load='3ski' size='340' side='right'caption='[[3ski]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
<StructureSection load='3ski' size='340' side='right'caption='[[3ski]], [[Resolution|resolution]] 2.30&Aring;' 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 [https://proteopedia.org/fgij/fg.htm?mol=3SKI FirstGlance]. <br>
<table><tr><td colspan='2'>[[3ski]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mesoplasma_florum Mesoplasma florum]. 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" 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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GNG:2-DEOXY-GUANOSINE'>GNG</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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='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'>[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>
<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;">
== Publication Abstract from PubMed ==
Purine 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<ref>PMID:21841796</ref>
==See Also==
 
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3ski" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Patel, D J]]
[[Category: Mesoplasma florum]]
[[Category: Pikovskaya, O]]
[[Category: Patel DJ]]
[[Category: Polonskaia, A]]
[[Category: Pikovskaya O]]
[[Category: Serganov, A]]
[[Category: Polonskaia A]]
[[Category: Deoxyguanosine]]
[[Category: Serganov A]]
[[Category: Riboswitch]]
[[Category: Rna]]
[[Category: Three-way junction]]

Latest revision as of 12:51, 1 March 2024

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosineCrystal structure of the 2'- Deoxyguanosine riboswitch bound to 2'-deoxyguanosine

Structural highlights

3ski is a 2 chain structure with sequence from Mesoplasma florum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:, , , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3ski, resolution 2.30Å

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