3v7e: Difference between revisions

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<StructureSection load='3v7e' size='340' side='right'caption='[[3v7e]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
<StructureSection load='3v7e' size='340' side='right'caption='[[3v7e]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3v7e]] is a 4 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=3V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7E FirstGlance]. <br>
<table><tr><td colspan='2'>[[3v7e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3V7E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3V7E FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</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]] 2.8&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3v7q|3v7q]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BSU01090, rplGB, ybaB, ybxF ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [https://pdbe.org/3v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [https://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e 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=3v7e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3v7e OCA], [https://pdbe.org/3v7e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3v7e RCSB], [https://www.ebi.ac.uk/pdbsum/3v7e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3v7e ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[https://www.uniprot.org/uniprot/RXL7_BACSU RXL7_BACSU]
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.


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>
==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 3v7e" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Vibrio subtilis ehrenberg 1835]]
[[Category: Bacillus subtilis]]
[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]]
[[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: A member of the l7ae/l30e superfamily]]
[[Category: K-turn]]
[[Category: K-turn motif]]
[[Category: L7ae-like]]
[[Category: Ribosomal protein-rna complex]]
[[Category: Riboswitch]]
[[Category: Rna-protein complex]]
[[Category: Unknown function]]

Latest revision as of 17:20, 14 March 2024

Crystal structure of YbxF bound to the SAM-I riboswitch aptamerCrystal structure of YbxF bound to the SAM-I riboswitch aptamer

Structural highlights

3v7e is a 4 chain structure with sequence from Bacillus subtilis and Caldanaerobacter subterraneus subsp. tengcongensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.8Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RXL7_BACSU

See Also

3v7e, resolution 2.80Å

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