7vnv: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
Line 3: Line 3:
<StructureSection load='7vnv' size='340' side='right'caption='[[7vnv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
<StructureSection load='7vnv' size='340' side='right'caption='[[7vnv]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7vnv]] 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=7VNV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNV FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNV FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</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]] 1.9&#8491;</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=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</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=9QV:uridine+2,5-bis(dihydrogen+phosphate)'>9QV</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>, <scene name='pdbligand=SUR:1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5-PHOSPHATE'>SUR</scene></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=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</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=9QV:uridine+2,5-bis(dihydrogen+phosphate)'>9QV</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>, <scene name='pdbligand=SUR:1-(BETA-D-RIBOFURANOSYL)-2-THIO-URACIL-5-PHOSPHATE'>SUR</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=7vnv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnv OCA], [https://pdbe.org/7vnv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnv RCSB], [https://www.ebi.ac.uk/pdbsum/7vnv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnv 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=7vnv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnv OCA], [https://pdbe.org/7vnv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnv RCSB], [https://www.ebi.ac.uk/pdbsum/7vnv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnv 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.
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>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7vnv" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Sulfurisphaera tokodaii]]
[[Category: Ohira T]]
[[Category: Ohira T]]
[[Category: Suzuki T]]
[[Category: Suzuki T]]
[[Category: Tomtia K]]
[[Category: Tomtia K]]
[[Category: Yamashita S]]
[[Category: Yamashita S]]

Latest revision as of 13:48, 1 July 2026

Crystal Structure of tRNAVal from Sulfolobus Tokodaii

7vnv, resolution 1.90Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=7vnv&oldid=4462870"