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| | <StructureSection load='2eew' size='340' side='right'caption='[[2eew]], [[Resolution|resolution]] 2.25Å' scene=''> | | <StructureSection load='2eew' size='340' side='right'caption='[[2eew]], [[Resolution|resolution]] 2.25Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2eew]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EEW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EEW FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2eew]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EEW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EEW FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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]] 2.25Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1u8d|1u8d]], [[2ees|2ees]], [[2eet|2eet]], [[2eeu|2eeu]], [[2eev|2eev]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></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=2eew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eew OCA], [http://pdbe.org/2eew PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2eew RCSB], [http://www.ebi.ac.uk/pdbsum/2eew PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2eew 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=2eew FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2eew OCA], [https://pdbe.org/2eew PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2eew RCSB], [https://www.ebi.ac.uk/pdbsum/2eew PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2eew 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: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Batey, R T]] | + | [[Category: Batey RT]] |
| - | [[Category: Gilbert, S D]] | + | [[Category: Gilbert SD]] |
| - | [[Category: Love, C E]] | + | [[Category: Love CE]] |
| - | [[Category: Base triple]]
| + | |
| - | [[Category: Guanine]]
| + | |
| - | [[Category: Hypoxanthine]]
| + | |
| - | [[Category: Mrna]]
| + | |
| - | [[Category: Riboswitch]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Rna-ligand complex]]
| + | |
| - | [[Category: Three-way junction]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The purine riboswitch is one of a number of mRNA elements commonly found in the 5'-untranslated region capable of controlling expression in a cis-fashion via its ability to directly bind small-molecule metabolites. Extensive biochemical and structural analysis of the nucleobase-binding domain of the riboswitch, referred to as the aptamer domain, has revealed that the mRNA recognizes its cognate ligand using an intricately folded three-way junction motif that completely encapsulates the ligand. High-affinity binding of the purine nucleobase is facilitated by a distal loop-loop interaction that is conserved between both the adenine and guanine riboswitches. To understand the contribution of conserved nucleotides in both the three-way junction and the loop-loop interaction of this RNA, we performed a detailed mutagenic survey of these elements in the context of an adenine-responsive variant of the xpt-pbuX guanine riboswitch from Bacillus subtilis. The varying ability of these mutants to bind ligand as measured by isothermal titration calorimetry uncovered the conserved nucleotides whose identity is required for purine binding. Crystallographic analysis of the bound form of five mutants and chemical probing of their free state demonstrate that the identity of several universally conserved nucleotides is not essential for formation of the RNA-ligand complex but rather for maintaining a binding-competent form of the free RNA. These data show that conservation patterns in riboswitches arise from a combination of formation of the ligand-bound complex, promoting an open form of the free RNA, and participating in the secondary structural switch with the expression platform.
Mutational analysis of the purine riboswitch aptamer domain.,Gilbert SD, Love CE, Edwards AL, Batey RT Biochemistry. 2007 Nov 20;46(46):13297-309. Epub 2007 Oct 26. PMID:17960911[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Gilbert SD, Love CE, Edwards AL, Batey RT. Mutational analysis of the purine riboswitch aptamer domain. Biochemistry. 2007 Nov 20;46(46):13297-309. Epub 2007 Oct 26. PMID:17960911 doi:10.1021/bi700410g
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