7vnx - Revision history

OCA at 19:43, 29 May 2024

OCA — Wed, 29 May 2024 19:43:18 GMT

←Older revision		Revision as of 19:43, 29 May 2024
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	==Crystal structure of TkArkI==		==Crystal structure of TkArkI==
-	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]]' scene=''>	+	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>		<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>
-	</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx ProSAT]</span></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]] 1.801Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 14:54, 31 August 2022

OCA — Wed, 31 Aug 2022 14:54:40 GMT

←Older revision		Revision as of 14:54, 31 August 2022
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	==Crystal structure of TkArkI==		==Crystal structure of TkArkI==
-	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]]~~, [[Resolution\|resolution]] 1.80Å~~' scene=''>	+	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[7vnx]] is a 1 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>
-	</td></tr>~~<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</scene></td></tr>~~	+	</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx 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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 7vnx" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Minowa, K]]	+	[[Category: Minowa K]]
-	[[Category: Ohira, T]]	+	[[Category: Ohira T]]
-	[[Category: Suzuki, T]]	+	[[Category: Suzuki T]]
-	[[Category: Tomita, K]]	+	[[Category: Tomita K]]
-	[[Category: Yamashita, S]]	+	[[Category: Yamashita S]]
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 06:37, 12 May 2022

OCA — Thu, 12 May 2022 06:37:02 GMT

←Older revision		Revision as of 06:37, 12 May 2022
Line 1:		Line 1:

	==Crystal structure of TkArkI==		==Crystal structure of TkArkI==
-	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]]' scene=''>	+	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vnx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>
-	</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GMP:GUANOSINE'>GMP</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vnx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Minowa K]]	+	[[Category: Minowa, K]]
-	[[Category: Ohira T]]	+	[[Category: Ohira, T]]
-	[[Category: Suzuki T]]	+	[[Category: Suzuki, T]]
-	[[Category: Tomita K]]	+	[[Category: Tomita, K]]
-	[[Category: Yamashita S]]	+	[[Category: Yamashita, S]]
		+	[[Category: Kinase]]
		+	[[Category: Rna binding protein]]

OCA at 12:54, 4 May 2022

OCA — Wed, 04 May 2022 12:54:11 GMT

←Older revision		Revision as of 12:54, 4 May 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7vnx is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of TkArkI==
-		+	<StructureSection load='7vnx' size='340' side='right'caption='[[7vnx]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VNX FirstGlance]. <br>
-	~~Description~~:	+	</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=7vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vnx OCA], [https://pdbe.org/7vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vnx RCSB], [https://www.ebi.ac.uk/pdbsum/7vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vnx ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Minowa K]]
		+	[[Category: Ohira T]]
		+	[[Category: Suzuki T]]
		+	[[Category: Tomita K]]
		+	[[Category: Yamashita S]]

OCA at 12:49, 27 October 2021

OCA — Wed, 27 Oct 2021 12:49:41 GMT

←Older revision		Revision as of 12:49, 27 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vnx is ON HOLD	+	The entry 7vnx is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7vnx" [edit=sysop:move=sysop]

OCA — Wed, 20 Oct 2021 15:17:16 GMT

Protected "7vnx" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:17, 20 October 2021

OCA: New page: '''Unreleased structure''' The entry 7vnx is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 20 Oct 2021 15:17:15 GMT

New page: '''Unreleased structure''' The entry 7vnx is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7vnx is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]