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| | ==Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA== | | ==Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA== |
| - | <StructureSection load='4lck' size='340' side='right' caption='[[4lck]], [[Resolution|resolution]] 3.20Å' scene=''> | + | <StructureSection load='4lck' size='340' side='right'caption='[[4lck]], [[Resolution|resolution]] 3.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4lck]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LCK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LCK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4lck]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis_subsp._subtilis_str._168 Bacillus subtilis subsp. subtilis str. 168] and [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis Oceanobacillus iheyensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LCK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LCK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 3.2Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rplGB, ybaB, ybxF, BSU01090 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 Bacillus subtilis subsp. subtilis str. 168])</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=4lck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lck OCA], [https://pdbe.org/4lck PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lck RCSB], [https://www.ebi.ac.uk/pdbsum/4lck PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lck 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=4lck FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lck OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4lck RCSB], [http://www.ebi.ac.uk/pdbsum/4lck PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/RXL7_BACSU RXL7_BACSU] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 4lck" style="background-color:#fffaf0;"></div> |
| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Riboswitch|Riboswitch]] | + | *[[Riboswitch 3D structures|Riboswitch 3D structures]] |
| | + | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Bacillus subtilis subsp. subtilis str. 168]] | | [[Category: Bacillus subtilis subsp. subtilis str. 168]] |
| - | [[Category: Amare, A R.Ferre-D]] | + | [[Category: Large Structures]] |
| - | [[Category: Zhang, J]] | + | [[Category: Oceanobacillus iheyensis]] |
| - | [[Category: Bacteria]] | + | [[Category: Ferre-D'Amare AR]] |
| - | [[Category: Gene expression regulation]]
| + | [[Category: Zhang J]] |
| - | [[Category: Ribosomal protein-rna complex]]
| + | |
| - | [[Category: Riboswitch mrna]] | + | |
| - | [[Category: Trna-mrna complex]]
| + | |
| Structural highlights
Function
RXL7_BACSU
Publication Abstract from PubMed
In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states. T-boxes reside in the 5'-untranslated regions of the messenger RNAs they regulate, and consist of two conserved domains. Stem I contains the specifier trinucleotide that base pairs with the anticodon of cognate tRNA. 3' to stem I is the antiterminator domain, which base pairs with the tRNA acceptor end and evaluates its aminoacylation state. Despite high phylogenetic conservation and widespread occurrence in pathogens, the structural basis of tRNA recognition by this riboswitch remains ill defined. Here we demonstrate that the ~100-nucleotide T-box stem I is necessary and sufficient for specific, high-affinity (dissociation constant (Kd) ~150 nM) tRNA binding, and report the structure of Oceanobacillus iheyensis glyQ stem I in complex with its cognate tRNA at 3.2 A resolution. Stem I recognizes the overall architecture of tRNA in addition to its anticodon, something accomplished by large ribonucleoproteins such as the ribosome, or proteins such as aminoacyl-tRNA synthetases, but is unprecedented for a compact mRNA domain. The C-shaped stem I cradles the L-shaped tRNA, forming an extended (1,604 A(2)) intermolecular interface. In addition to the specifier-anticodon interaction, two interdigitated T-loops near the apex of stem I stack on the tRNA elbow in a manner analogous to those of the J11/12-J12/11 motif of RNase P and the L1 stalk of the ribosomal E-site. Because these ribonucleoproteins and T-boxes are unrelated, this strategy to recognize a universal tRNA feature probably evolved convergently. Mutually induced fit of stem I and the tRNA exploiting the intrinsic flexibility of tRNA and its conserved post-transcriptional modifications results in high shape complementarity, which in addition to providing specificity and affinity, globally organizes the T-box to orchestrate tRNA-dependent transcription regulation.
Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA.,Zhang J, Ferre-D'Amare AR Nature. 2013 Aug 15;500(7462):363-6. doi: 10.1038/nature12440. Epub 2013 Jul 28. PMID:23892783[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Zhang J, Ferre-D'Amare AR. Co-crystal structure of a T-box riboswitch stem I domain in complex with its cognate tRNA. Nature. 2013 Aug 15;500(7462):363-6. doi: 10.1038/nature12440. Epub 2013 Jul 28. PMID:23892783 doi:10.1038/nature12440
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