5mq9 - Revision history

OCA at 17:44, 8 November 2023

2023-11-08T17:44:14Z

←Older revision		Revision as of 17:44, 8 November 2023
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	<StructureSection load='5mq9' size='340' side='right'caption='[[5mq9]], [[Resolution\|resolution]] 3.17Å' scene=''>		<StructureSection load='5mq9' size='340' side='right'caption='[[5mq9]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bacsu Bacsu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure with sequence from [https://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=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 3.174Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~yacP, BSU00970 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=224308 BACSU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [~~http~~://pdbe.org/5mq9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 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=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [https://pdbe.org/5mq9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [https://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/YACP_BACSU YACP_BACSU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacsu~~]]	+	[[Category: Bacillus subtilis subsp. subtilis str. 168]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Condon, C]]	+	[[Category: Condon C]]
-	[[Category: Figaro, S]]	+	[[Category: Figaro S]]
-	[[Category: Gilet, L]]	+	[[Category: Gilet L]]
-	[[Category: Leroy, M]]	+	[[Category: Leroy M]]
-	[[Category: Pellegrini, O]]	+	[[Category: Pellegrini O]]
-	[[Category: Piton, J]]	+	[[Category: Piton J]]
-	~~[[Category: B. subtili]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Peptide toxin]]~~	+
-	~~[[Category: Rna maturation and decay]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 06:37, 16 October 2019

2019-10-16T06:37:46Z

←Older revision		Revision as of 06:37, 16 October 2019
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	==Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)==		==Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)==
-	<StructureSection load='5mq9' size='340' side='right' caption='[[5mq9]], [[Resolution\|resolution]] 3.17Å' scene=''>	+	<StructureSection load='5mq9' size='340' side='right'caption='[[5mq9]], [[Resolution\|resolution]] 3.17Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacsu Bacsu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">yacP, BSU00970 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224308 BACSU])</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=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [http://pdbe.org/5mq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [http://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 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=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [http://pdbe.org/5mq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [http://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacsu]]
		+	[[Category: Large Structures]]
	[[Category: Condon, C]]		[[Category: Condon, C]]
	[[Category: Figaro, S]]		[[Category: Figaro, S]]

OCA at 13:01, 19 April 2017

2017-04-19T13:01:02Z

←Older revision		Revision as of 13:01, 19 April 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5mq9 is ~~ON HOLD~~	+	==Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)==
		+	<StructureSection load='5mq9' size='340' side='right' caption='[[5mq9]], [[Resolution\|resolution]] 3.17Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5mq9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MQ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MQ9 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5mq9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mq9 OCA], [http://pdbe.org/5mq9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mq9 RCSB], [http://www.ebi.ac.uk/pdbsum/5mq9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mq9 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The PIN domain plays a central role in cellular RNA biology and is involved in processes as diverse as rRNA maturation, mRNA decay and telomerase function. Here, we solve the crystal structure of the Rae1 (YacP) protein of Bacillus subtilis, a founding member of the NYN (Nedd4-BP1/YacP nuclease) subfamily of PIN domain proteins, and identify potential substrates in vivo Unexpectedly, degradation of a characterised target mRNA was completely dependent on both its translation and reading frame. We provide evidence that Rae1 associates with the B. subtilis ribosome and cleaves between specific codons of this mRNA in vivo Critically, we also demonstrate translation-dependent Rae1 cleavage of this substrate in a purified translation assay in vitro Multiple lines of evidence converge to suggest that Rae1 is an A-site endoribonuclease. We present a docking model of Rae1 bound to the B. subtilis ribosomal A-site that is consistent with this hypothesis and show that Rae1 cleaves optimally immediately upstream of a lysine codon (AAA or AAG) in vivo.

-	~~Authors: Piton~~, J., ~~Gilet~~, L., Pellegrini, O., ~~Leroy~~, M., Figaro, S., Condon, C.	+	Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis.,Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppee JY, Figaro S, Condon C EMBO J. 2017 Mar 31. pii: e201796540. doi: 10.15252/embj.201796540. PMID:28363943<ref>PMID:28363943</ref>

-	~~Description: Crystal structure~~ of ~~Rae1 (YacP) from Bacillus subtilis (W164L mutant)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	[[Category: ~~Piton~~, J]]	+	<div class="pdbe-citations 5mq9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Condon, C]]
	[[Category: Figaro, S]]		[[Category: Figaro, S]]
-	[[Category: Pellegrini, O]]
	[[Category: Gilet, L]]		[[Category: Gilet, L]]
-	[[Category: Condon, C]]
	[[Category: Leroy, M]]		[[Category: Leroy, M]]
		+	[[Category: Pellegrini, O]]
		+	[[Category: Piton, J]]
		+	[[Category: B. subtili]]
		+	[[Category: Endonuclease]]
		+	[[Category: Peptide toxin]]
		+	[[Category: Rna maturation and decay]]
		+	[[Category: Translation]]

OCA at 11:32, 9 March 2017

2017-03-09T11:32:37Z

←Older revision		Revision as of 11:32, 9 March 2017
Line 7:		Line 7:
	Description: Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)		Description: Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Figaro, S]]
-	[[Category: Condon, C]]
	[[Category: Piton, J]]		[[Category: Piton, J]]
		+	[[Category: Figaro, S]]
	[[Category: Pellegrini, O]]		[[Category: Pellegrini, O]]
	[[Category: Gilet, L]]		[[Category: Gilet, L]]
		+	[[Category: Condon, C]]
	[[Category: Leroy, M]]		[[Category: Leroy, M]]

OCA: Protected "5mq9" [edit=sysop:move=sysop]

2017-01-02T13:51:46Z

Protected "5mq9" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:51, 2 January 2017

OCA: New page: '''Unreleased structure''' The entry 5mq9 is ON HOLD Authors: Piton, J., Gilet, L., Pellegrini, O., Leroy, M., Figaro, S., Condon, C. Description: Crystal structure of Rae1 (YacP) from...

2017-01-02T13:51:45Z

New page: '''Unreleased structure''' The entry 5mq9 is ON HOLD Authors: Piton, J., Gilet, L., Pellegrini, O., Leroy, M., Figaro, S., Condon, C. Description: Crystal structure of Rae1 (YacP) from...

New page

'''Unreleased structure'''

The entry 5mq9 is ON HOLD

Authors: Piton, J., Gilet, L., Pellegrini, O., Leroy, M., Figaro, S., Condon, C.

Description: Crystal structure of Rae1 (YacP) from Bacillus subtilis (W164L mutant)
[[Category: Unreleased Structures]]
[[Category: Figaro, S]]
[[Category: Condon, C]]
[[Category: Piton, J]]
[[Category: Pellegrini, O]]
[[Category: Gilet, L]]
[[Category: Leroy, M]]