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==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate==
==Crystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate==
<StructureSection load='3slq' size='340' side='right' caption='[[3slq]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
<StructureSection load='3slq' size='340' side='right'caption='[[3slq]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3slq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SLQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SLQ FirstGlance]. <br>
<table><tr><td colspan='2'>[[3slq]] 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=3SLQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SLQ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</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]] 2.5&#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=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=CCC:CYTIDINE-5-PHOSPHATE-2,3-CYCLIC+PHOSPHATE'>CCC</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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">[[3skz|3skz]], [[3slm|3slm]], [[3ski|3ski]], [[3skw|3skw]], [[3skt|3skt]], [[3skl|3skl]]</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=3slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3slq OCA], [https://pdbe.org/3slq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3slq RCSB], [https://www.ebi.ac.uk/pdbsum/3slq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3slq ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3slq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3slq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3slq RCSB], [http://www.ebi.ac.uk/pdbsum/3slq PDBsum]</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>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
==See Also==
</div>
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Patel, D J]]
[[Category: Large Structures]]
[[Category: Pikovskaya, O]]
[[Category: Mesoplasma florum]]
[[Category: Polonskaia, A]]
[[Category: Patel DJ]]
[[Category: Serganov, A]]
[[Category: Pikovskaya O]]
[[Category: 2'-deoxy guanosine]]
[[Category: Polonskaia A]]
[[Category: Riboswitch]]
[[Category: Serganov A]]
[[Category: Rna]]
[[Category: Three-way junction]]

Latest revision as of 12:51, 1 March 2024

Crystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphateCrystal structure of the 2'- Deoxyguanosine riboswitch bound to guanosine-5'-monophosphate

Structural highlights

3slq 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 2.5Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3slq, resolution 2.50Å

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