6y2q - Revision history

OCA at 13:18, 24 January 2024

OCA — Wed, 24 Jan 2024 13:18:10 GMT

←Older revision		Revision as of 13:18, 24 January 2024
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	<StructureSection load='6y2q' size='340' side='right'caption='[[6y2q]], [[Resolution\|resolution]] 2.99Å' scene=''>		<StructureSection load='6y2q' size='340' side='right'caption='[[6y2q]], [[Resolution\|resolution]] 2.99Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y2Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y2Q FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2.99Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~rnlA, std, yfjN, b2630, JW2611 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=6y2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y2q OCA], [https://pdbe.org/6y2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y2q RCSB], [https://www.ebi.ac.uk/pdbsum/6y2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y2q 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=6y2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y2q OCA], [https://pdbe.org/6y2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y2q RCSB], [https://www.ebi.ac.uk/pdbsum/6y2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y2q ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>	+	[https://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>
	<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: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia-Rodriguez, G]]	+	[[Category: Garcia-Rodriguez G]]
-	[[Category: Loris, R]]	+	[[Category: Loris R]]
-	~~[[Category: Endoribonuclease]]~~	+
-	~~[[Category: Hepn protein]]~~	+
-	~~[[Category: T4 phage denfense]]~~	+
-	~~[[Category: Toxin]]~~	+
-	~~[[Category: Toxin-antitoxin system~~]]	+

OCA at 09:08, 21 July 2021

OCA — Wed, 21 Jul 2021 09:08:04 GMT

←Older revision		Revision as of 09:08, 21 July 2021
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	==Escherichia coli RnlA endoribonuclease==		==Escherichia coli RnlA endoribonuclease==
-	<StructureSection load='6y2q' size='340' side='right'caption='[[6y2q]]' scene=''>	+	<StructureSection load='6y2q' size='340' side='right'caption='[[6y2q]], [[Resolution\|resolution]] 2.99Å' 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=6Y2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y2Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y2q]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y2Q 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=6y2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y2q OCA], [https://pdbe.org/6y2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y2q RCSB], [https://www.ebi.ac.uk/pdbsum/6y2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y2q 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=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rnlA, std, yfjN, b2630, JW2611 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6y2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y2q OCA], [https://pdbe.org/6y2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y2q RCSB], [https://www.ebi.ac.uk/pdbsum/6y2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y2q ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/RNLA_ECOLI RNLA_ECOLI]] Toxic component of a toxin-antitoxin (TA) module. A stable (half-life 27.6 minutes) endoribonuclease that in the absence of cognate antitoxin RnlB causes generalized RNA degradation. Degrades late enterobacteria phage T4 mRNAs, protecting the host against T4 reproduction. Activity is inhibited by cognate antitoxin RnlB and by enterobacteria phage T4 protein Dmd. Targets cyaA mRNA.<ref>PMID:17895580</ref> <ref>PMID:19019153</ref> <ref>PMID:20980243</ref> <ref>PMID:22403819</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The rnlAB toxin-antitoxin operon from Escherichia coli functions as an anti-phage defense system. RnlA was identified as a member of the HEPN (Higher Eukaryotes and Prokaryotes Nucleotide-binding domain) superfamily of ribonucleases. The activity of the toxin RnlA requires tight regulation by the antitoxin RnlB, the mechanism of which remains unknown. Here we show that RnlA exists in an equilibrium between two different homodimer states: an inactive resting state and an active canonical HEPN dimer. Mutants interfering with the transition between states show that canonical HEPN dimerization via the highly conserved RX4-6H motif is required for activity. The antitoxin RnlB binds the canonical HEPN dimer conformation, inhibiting RnlA by blocking access to its active site. Single-alanine substitutions mutants of the highly conserved R255, E258, R318 and H323 show that these residues are involved in catalysis and substrate binding and locate the catalytic site near the dimer interface of the canonical HEPN dimer rather than in a groove located between the HEPN domain and the preceding TBP-like domain. Overall, these findings elucidate the structural basis of the activity and inhibition of RnlA and highlight the crucial role of conformational heterogeneity in protein function.
		+
		+	Alternative dimerization is required for activity and inhibition of the HEPN ribonuclease RnlA.,Garcia-Rodriguez G, Charlier D, Wilmaerts D, Michiels J, Loris R Nucleic Acids Res. 2021 Jul 9;49(12):7164-7178. doi: 10.1093/nar/gkab513. PMID:34139012<ref>PMID:34139012</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y2q" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia-Rodriguez G]]	+	[[Category: Garcia-Rodriguez, G]]
-	[[Category: Loris R]]	+	[[Category: Loris, R]]
		+	[[Category: Endoribonuclease]]
		+	[[Category: Hepn protein]]
		+	[[Category: T4 phage denfense]]
		+	[[Category: Toxin]]
		+	[[Category: Toxin-antitoxin system]]

OCA at 09:18, 12 May 2021

OCA — Wed, 12 May 2021 09:18:08 GMT

←Older revision		Revision as of 09:18, 12 May 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6y2q ~~is ON HOLD until Paper Publication~~	+	==Escherichia coli RnlA endoribonuclease==
-		+	<StructureSection load='6y2q' size='340' side='right'caption='[[6y2q]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y2Q 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=6y2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y2q OCA], [https://pdbe.org/6y2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y2q RCSB], [https://www.ebi.ac.uk/pdbsum/6y2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y2q ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Garcia-Rodriguez G]]
		+	[[Category: Loris R]]

OCA at 04:07, 28 April 2021

OCA — Wed, 28 Apr 2021 04:07:48 GMT

←Older revision		Revision as of 04:07, 28 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y2q is ON HOLD	+	The entry 6y2q is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:25, 7 April 2021

OCA — Wed, 07 Apr 2021 04:25:06 GMT

←Older revision		Revision as of 04:25, 7 April 2021
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y2q is ON HOLD ~~until Paper Publication~~	+	The entry 6y2q is ON HOLD

	Authors:		Authors:

OCA at 05:42, 4 March 2020

OCA — Wed, 04 Mar 2020 05:42:38 GMT

←Older revision		Revision as of 05:42, 4 March 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y2q is ON HOLD	+	The entry 6y2q is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6y2q" [edit=sysop:move=sysop]

OCA — Wed, 26 Feb 2020 08:17:52 GMT

Protected "6y2q" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:17, 26 February 2020

OCA: New page: '''Unreleased structure''' The entry 6y2q is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 26 Feb 2020 08:17:51 GMT

New page: '''Unreleased structure''' The entry 6y2q is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y2q is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]