4o87 - Revision history

OCA at 12:38, 1 March 2024

OCA — Fri, 01 Mar 2024 12:38:13 GMT

←Older revision		Revision as of 12:38, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Millerozyma_acaciae Millerozyma acaciae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O87 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Millerozyma_acaciae Millerozyma acaciae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O87 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.8Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [https://pdbe.org/4o87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [https://www.ebi.ac.uk/pdbsum/4o87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o87 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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [https://pdbe.org/4o87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [https://www.ebi.ac.uk/pdbsum/4o87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o87 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/Q707V3_9ASCO Q707V3_9ASCO]		[https://www.uniprot.org/uniprot/Q707V3_9ASCO Q707V3_9ASCO]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	tRNA restriction by anticodon nucleases underlies cellular stress responses and self-nonself discrimination in a wide range of taxa. Anticodon breakage inhibits protein synthesis, which, in turn, results in growth arrest or cell death. The eukaryal ribotoxin PaT secreted by Pichia acaciae inhibits growth of Saccharomyces cerevisiae via cleavage of tRNA(Gln(UUG)). We find that recombinant PaT incises a synthetic tRNA(Gln(UUG)) stem-loop RNA by transesterification at a single site 3' of the wobble uridine, yielding 2',3'-cyclic phosphate and 5'-OH ends. Incision is suppressed by replacement of the wobble nucleobase with adenine or guanine. The crystal structure of PaT reveals a distinctive fold and active site, essential components of which are demonstrated by mutagenesis. Pichia acaciae evades self-toxicity via a distinctive intracellular immunity protein, ImmPaT, which binds PaT and blocks nuclease activity. Our results highlight the evolutionary diversity of tRNA restriction and immunity systems.
-
-	Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination.,Chakravarty AK, Smith P, Jalan R, Shuman S Cell Rep. 2014 Apr 24;7(2):339-47. doi: 10.1016/j.celrep.2014.03.034. Epub 2014, Apr 13. PMID:24726365<ref>PMID:24726365</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4o87" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:59, 18 January 2023

OCA — Wed, 18 Jan 2023 08:59:59 GMT

←Older revision		Revision as of 08:59, 18 January 2023
Line 3:		Line 3:
	<StructureSection load='4o87' size='340' side='right'caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4o87' size='340' side='right'caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_22303 Atcc 22303~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4O87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Millerozyma_acaciae Millerozyma acaciae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4O87 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]~~</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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [https://pdbe.org/4o87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [https://www.ebi.ac.uk/pdbsum/4o87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4o87 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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [~~http~~://pdbe.org/4o87 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4o87 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4o87 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q707V3_9ASCO Q707V3_9ASCO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 22303]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chakravarty, A K~~]]	+	[[Category: Millerozyma acaciae]]
-	[[Category: ~~Shuman, S~~]]	+	[[Category: Chakravarty AK]]
-	[[Category: ~~Smith, P~~]]	+	[[Category: Shuman S]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Smith P]]
-	~~[[Category: Novel fold]]~~	+
-	~~[[Category: Nuclease~~]]	+

OCA at 05:02, 13 February 2020

OCA — Thu, 13 Feb 2020 05:02:41 GMT

←Older revision		Revision as of 05:02, 13 February 2020
Line 1:		Line 1:

	==Crystal structure of a N-tagged Nuclease==		==Crystal structure of a N-tagged Nuclease==
-	<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4o87' size='340' side='right'caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_22303 Atcc 22303]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O87 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_22303 Atcc 22303]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O87 FirstGlance]. <br>
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 22303]]		[[Category: Atcc 22303]]
		+	[[Category: Large Structures]]
	[[Category: Chakravarty, A K]]		[[Category: Chakravarty, A K]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]

OCA at 08:22, 22 November 2017

OCA — Wed, 22 Nov 2017 08:22:06 GMT

←Older revision		Revision as of 08:22, 22 November 2017
Line 3:		Line 3:
	<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O87 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_22303 Atcc 22303]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O87 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]</td></tr>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 22303]]
	[[Category: Chakravarty, A K]]		[[Category: Chakravarty, A K]]
	[[Category: Shuman, S]]		[[Category: Shuman, S]]

OCA at 18:47, 11 August 2016

OCA — Thu, 11 Aug 2016 18:47:10 GMT

←Older revision		Revision as of 18:47, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a N-tagged Nuclease==		==Crystal structure of a N-tagged Nuclease==
	<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]</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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [http://www.ebi.ac.uk/pdbsum/4o87 PDBsum]</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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [http://pdbe.org/4o87 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [http://www.ebi.ac.uk/pdbsum/4o87 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4o87 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 16:
	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 4o87" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:05, 25 January 2015

OCA — Sun, 25 Jan 2015 08:05:33 GMT

←Older revision		Revision as of 08:05, 25 January 2015
Line 19:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Chakravarty, A K.]]	+	[[Category: Chakravarty, A K]]
-	[[Category: Shuman, S.]]	+	[[Category: Shuman, S]]
-	[[Category: Smith, P.]]	+	[[Category: Smith, P]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]
	[[Category: Novel fold]]		[[Category: Novel fold]]
	[[Category: Nuclease]]		[[Category: Nuclease]]

OCA at 10:44, 20 October 2014

OCA — Mon, 20 Oct 2014 10:44:38 GMT

←Older revision		Revision as of 10:44, 20 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of a N-tagged Nuclease==
		+	<StructureSection load='4o87' size='340' side='right' caption='[[4o87]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4o87]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4O87 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4O87 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4o88\|4o88]]</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=4o87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4o87 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4o87 RCSB], [http://www.ebi.ac.uk/pdbsum/4o87 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	tRNA restriction by anticodon nucleases underlies cellular stress responses and self-nonself discrimination in a wide range of taxa. Anticodon breakage inhibits protein synthesis, which, in turn, results in growth arrest or cell death. The eukaryal ribotoxin PaT secreted by Pichia acaciae inhibits growth of Saccharomyces cerevisiae via cleavage of tRNA(Gln(UUG)). We find that recombinant PaT incises a synthetic tRNA(Gln(UUG)) stem-loop RNA by transesterification at a single site 3' of the wobble uridine, yielding 2',3'-cyclic phosphate and 5'-OH ends. Incision is suppressed by replacement of the wobble nucleobase with adenine or guanine. The crystal structure of PaT reveals a distinctive fold and active site, essential components of which are demonstrated by mutagenesis. Pichia acaciae evades self-toxicity via a distinctive intracellular immunity protein, ImmPaT, which binds PaT and blocks nuclease activity. Our results highlight the evolutionary diversity of tRNA restriction and immunity systems.

-	~~The entry 4o87 is ON HOLD until Paper Publication~~	+	Structure, mechanism, and specificity of a eukaryal tRNA restriction enzyme involved in self-nonself discrimination.,Chakravarty AK, Smith P, Jalan R, Shuman S Cell Rep. 2014 Apr 24;7(2):339-47. doi: 10.1016/j.celrep.2014.03.034. Epub 2014, Apr 13. PMID:24726365<ref>PMID:24726365</ref>

-	~~Authors~~: Chakravarty, A.K., Smith, P.~~, Shuman, S.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of a N-tagged~~ Nuclease	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chakravarty, A K.]]
		+	[[Category: Shuman, S.]]
		+	[[Category: Smith, P.]]
		+	[[Category: Hydrolase]]
		+	[[Category: Novel fold]]
		+	[[Category: Nuclease]]

OCA at 08:23, 2 April 2014

OCA — Wed, 02 Apr 2014 08:23:49 GMT

←Older revision		Revision as of 08:23, 2 April 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4o87 is ON HOLD	+	The entry 4o87 is ON HOLD until Paper Publication

	Authors: Chakravarty, A.K., Smith, P., Shuman, S.		Authors: Chakravarty, A.K., Smith, P., Shuman, S.

	Description: Crystal structure of a N-tagged Nuclease		Description: Crystal structure of a N-tagged Nuclease

OCA at 07:42, 15 January 2014

OCA — Wed, 15 Jan 2014 07:42:31 GMT

←Older revision		Revision as of 07:42, 15 January 2014
Line 3:		Line 3:
	The entry 4o87 is ON HOLD		The entry 4o87 is ON HOLD

-	Authors: Chakravarty, A. K., Smith, P., Shuman, S.	+	Authors: Chakravarty, A.K., Smith, P., Shuman, S.

	Description: Crystal structure of a N-tagged Nuclease		Description: Crystal structure of a N-tagged Nuclease

OCA: Protected "4o87" [edit=sysop:move=sysop]

OCA — Wed, 08 Jan 2014 09:27:31 GMT

Protected "4o87" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:27, 8 January 2014