7vnw
From Proteopedia
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[7vnw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii Sulfurisphaera tokodaii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNW FirstGlance]. <br> | <table><tr><td colspan='2'>[[7vnw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii Sulfurisphaera tokodaii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNW FirstGlance]. <br> | ||
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.61Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=4AC:N(4)-ACETYLCYTIDINE-5-MONOPHOSPHATE'>4AC</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=7S3:[(2R,3S,4R,5R)-5-(1-methyl-6-oxidanylidene-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>7S3</scene>, <scene name='pdbligand=7SN:[(2R,3S,4R,5R)-5-(2-azanyl-5-carbamimidoyl-4-oxidanylidene-3H-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>7SN</scene>, <scene name='pdbligand=M2G:N2-DIMETHYLGUANOSINE-5-MONOPHOSPHATE'>M2G</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></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=7vnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnw OCA], [https://pdbe.org/7vnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnw RCSB], [https://www.ebi.ac.uk/pdbsum/7vnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnw 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=7vnw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnw OCA], [https://pdbe.org/7vnw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnw RCSB], [https://www.ebi.ac.uk/pdbsum/7vnw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnw ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Post-transcriptional modifications have critical roles in tRNA stability and function(1-4). In thermophiles, tRNAs are heavily modified to maintain their thermal stability under extreme growth temperatures(5,6). Here we identified 2'-phosphouridine (U(p)) at position 47 of tRNAs from thermophilic archaea. U(p)47 confers thermal stability and nuclease resistance to tRNAs. Atomic structures of native archaeal tRNA showed a unique metastable core structure stabilized by U(p)47. The 2'-phosphate of U(p)47 protrudes from the tRNA core and prevents backbone rotation during thermal denaturation. In addition, we identified the arkI gene, which encodes an archaeal RNA kinase responsible for U(p)47 formation. Structural studies showed that ArkI has a non-canonical kinase motif surrounded by a positively charged patch for tRNA binding. A knockout strain of arkI grew slowly at high temperatures and exhibited a synthetic growth defect when a second tRNA-modifying enzyme was depleted. We also identified an archaeal homologue of KptA as an eraser that efficiently dephosphorylates U(p)47 in vitro and in vivo. Taken together, our findings show that U(p)47 is a reversible RNA modification mediated by ArkI and KptA that fine-tunes the structural rigidity of tRNAs under extreme environmental conditions. | ||
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| - | Reversible RNA phosphorylation stabilizes tRNA for cellular thermotolerance.,Ohira T, Minowa K, Sugiyama K, Yamashita S, Sakaguchi Y, Miyauchi K, Noguchi R, Kaneko A, Orita I, Fukui T, Tomita K, Suzuki T Nature. 2022 Apr 27. pii: 10.1038/s41586-022-04677-2. doi:, 10.1038/s41586-022-04677-2. PMID:35477761<ref>PMID:35477761</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 7vnw" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Sulfurisphaera tokodaii]] | [[Category: Sulfurisphaera tokodaii]] | ||
| - | [[Category: Ohira | + | [[Category: Ohira T]] |
| - | [[Category: Suzuki | + | [[Category: Suzuki T]] |
| - | [[Category: Tomtia | + | [[Category: Tomtia K]] |
| - | [[Category: Yamashita | + | [[Category: Yamashita S]] |
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Current revision
Crystal Structure of tRNAVal from Sulfolobus Tokodaii(Dephosphorylated)
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