7aex - Revision history

OCA at 12:08, 1 February 2024

2024-02-01T12:08:18Z

←Older revision		Revision as of 12:08, 1 February 2024
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	<StructureSection load='7aex' size='340' side='right'caption='[[7aex]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='7aex' size='340' side='right'caption='[[7aex]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7aex]] is a 1 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=7AEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AEX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7aex]] is a 1 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=7AEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AEX FirstGlance]. <br>
-	</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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</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=7aex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aex OCA], [https://pdbe.org/7aex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aex RCSB], [https://www.ebi.ac.uk/pdbsum/7aex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aex 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=7aex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aex OCA], [https://pdbe.org/7aex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aex RCSB], [https://www.ebi.ac.uk/pdbsum/7aex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aex 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 09:11, 21 July 2021

2021-07-21T09:11:29Z

←Older revision		Revision as of 09:11, 21 July 2021
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	==NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease==		==NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease==
-	<StructureSection load='7aex' size='340' side='right'caption='[[7aex]]' scene=''>	+	<StructureSection load='7aex' size='340' side='right'caption='[[7aex]], [[Resolution\|resolution]] 1.95Å' 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=7AEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AEX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7aex]] is a 1 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=7AEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AEX 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=7aex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aex OCA], [https://pdbe.org/7aex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aex RCSB], [https://www.ebi.ac.uk/pdbsum/7aex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aex ProSAT]</span></td></tr>	+	</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=7aex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aex OCA], [https://pdbe.org/7aex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aex RCSB], [https://www.ebi.ac.uk/pdbsum/7aex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aex 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 7aex" 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 12:11, 9 June 2021

2021-06-09T12:11:33Z

←Older revision		Revision as of 12:11, 9 June 2021
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-	'''Unreleased structure'''

-	~~The entry 7aex is ON HOLD until Paper Publication~~	+	==NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease==
-		+	<StructureSection load='7aex' size='340' side='right'caption='[[7aex]]' scene=''>
-	~~Authors: Garcia-Rodriguez, G., Loris, R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7AEX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7AEX FirstGlance]. <br>
-	~~Description:~~ NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease	+	</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=7aex FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7aex OCA], [https://pdbe.org/7aex PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7aex RCSB], [https://www.ebi.ac.uk/pdbsum/7aex PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7aex ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Garcia-Rodriguez, G]]	+	__TOC__
-	[[Category: Loris, R]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Garcia-Rodriguez G]]
		+	[[Category: Loris R]]

OCA at 04:08, 28 April 2021

2021-04-28T04:08:02Z

←Older revision		Revision as of 04:08, 28 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Garcia-Rodriguez, G., Loris, R.		Authors: Garcia-Rodriguez, G., Loris, R.

OCA at 04:25, 7 April 2021

2021-04-07T04:25:55Z

←Older revision		Revision as of 04:25, 7 April 2021
Line 7:		Line 7:
	Description: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease		Description: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Loris, R]]
	[[Category: Garcia-Rodriguez, G]]		[[Category: Garcia-Rodriguez, G]]
		+	[[Category: Loris, R]]

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

2020-09-23T08:49:25Z

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

←Older revision

Revision as of 08:49, 23 September 2020

OCA: New page: '''Unreleased structure''' The entry 7aex is ON HOLD Authors: Garcia-Rodriguez, G., Loris, R. Description: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuc...

2020-09-23T08:49:22Z

New page: '''Unreleased structure''' The entry 7aex is ON HOLD Authors: Garcia-Rodriguez, G., Loris, R. Description: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuc...

New page

'''Unreleased structure'''

The entry 7aex is ON HOLD

Authors: Garcia-Rodriguez, G., Loris, R.

Description: NRD-HEPN domains (N-terminal truncation) of Escherichia coli RnlA endoribonuclease
[[Category: Unreleased Structures]]
[[Category: Loris, R]]
[[Category: Garcia-Rodriguez, G]]