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| | <StructureSection load='3v7q' size='340' side='right'caption='[[3v7q]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='3v7q' size='340' side='right'caption='[[3v7q]], [[Resolution|resolution]] 1.55Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3v7q]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3v7q]] is a 3 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=3V7Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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]] 1.55Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3v7e|3v7e]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU16620, rplGA, ylxQ, ymxC ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
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| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3v7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7q OCA], [https://pdbe.org/3v7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7q RCSB], [https://www.ebi.ac.uk/pdbsum/3v7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7q 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=3v7q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7q OCA], [https://pdbe.org/3v7q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7q RCSB], [https://www.ebi.ac.uk/pdbsum/3v7q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7q ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/YLXQ_BACSU YLXQ_BACSU]] RNA-binding protein that recognizes the K-turn motif present in ribosomal RNA, but also in box C/D and box C'/D' sRNAs.<ref>PMID:22355167</ref>
| + | [https://www.uniprot.org/uniprot/YLXQ_BACSU YLXQ_BACSU] RNA-binding protein that recognizes the K-turn motif present in ribosomal RNA, but also in box C/D and box C'/D' sRNAs.<ref>PMID:22355167</ref> |
| - | <div style="background-color:#fffaf0;">
| + | |
| - | == Publication Abstract from PubMed ==
| + | |
| - | The archaeal protein L7Ae and eukaryotic homologs such as L30e and 15.5kD comprise the best characterized family of K-turn-binding proteins. K-turns are an RNA motif comprised of a bulge flanked by canonical and noncanonical helices. They are widespread in cellular RNAs, including bacterial gene-regulatory RNAs such as the c-di-GMP-II, lysine, and SAM-I riboswitches, and the T-box. The existence in bacteria of K-turn-binding proteins of the L7Ae family has not been proven, although two hypothetical proteins, YbxF and YlxQ, have been proposed to be L7Ae homologs based on sequence conservation. Using purified, recombinant proteins, we show that Bacillus subtilis YbxF and YlxQ bind K-turns (K(d) approximately 270 nM and approximately 2300 nM, respectively). Crystallographic structure determination demonstrates that both YbxF and YlxQ adopt the same overall fold as L7Ae. Unlike the latter, neither bacterial protein recognizes K-loops, a structural motif that lacks the canonical helix of the K-turn. This property is shared between the bacterial and eukaryal family members. Comparison of our structure of YbxF in complex with the K-turn of the SAM-I riboswitch and previously determined structures of archaeal and eukaryal homologs bound to RNA indicates that L7Ae approaches the K-turn at a unique angle, which results in a considerably larger RNA-protein interface dominated by interactions with the noncanonical helix of the K-turn. Thus, the inability of the bacterial and eukaryal L7Ae homologs to bind K-loops probably results from their reliance on interactions with the canonical helix. The biological functions of YbxF and YlxQ remain to be determined.
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| - | YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops.,Baird NJ, Zhang J, Hamma T, Ferre-D'Amare AR RNA. 2012 Feb 21. PMID:22355167<ref>PMID:22355167</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 3v7q" style="background-color:#fffaf0;"></div>
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| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Amare, A R.Ferre-D]] | + | [[Category: Baird NJ]] |
| - | [[Category: Baird, N J]] | + | [[Category: Ferre-D'Amare AR]] |
| - | [[Category: Hamma, T]] | + | [[Category: Hamma T]] |
| - | [[Category: Zhang, J]] | + | [[Category: Zhang J]] |
| - | [[Category: Hypothetical ribosomal protein]]
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| - | [[Category: K-turn binding]]
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| - | [[Category: K-turn rna]]
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| - | [[Category: L7ae superfamily]]
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| - | [[Category: Rna binding protein]]
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