5f6c - Revision history

OCA at 06:39, 19 July 2023

2023-07-19T06:39:51Z

←Older revision		Revision as of 06:39, 19 July 2023
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	==The structure of E. coli RNase E catalytically inactive mutant with RNA bound==		==The structure of E. coli RNase E catalytically inactive mutant with RNA bound==
-	<StructureSection load='5f6c' size='340' side='right' caption='[[5f6c]], [[Resolution\|resolution]] 3.00Å' scene=''>	+	<StructureSection load='5f6c' size='340' side='right'caption='[[5f6c]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f6c]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6C OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5F6C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f6c]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [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=5F6C OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5F6C FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=MG:MAGNESIUM+ION'>MG</scene~~>, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 3.002Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>rne, ams, hmp1, b1084, JW1071 ([http://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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Ribonuclease_E Ribonuclease E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.12 3.1.26.12]~~ </~~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=5f6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6c OCA], [https://pdbe.org/5f6c PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5f6c RCSB], [https://www.ebi.ac.uk/pdbsum/5f6c PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6c 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=5f6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6c OCA], [~~http~~://pdbe.org/5f6c PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5f6c RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5f6c PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6c ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.	+	[https://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli]]
-	[[Category: ~~Ribonuclease E]]~~	+	[[Category: Escherichia coli K-12]]
-	~~[[Category: Bandyra,~~ K J]]	+	[[Category: Large Structures]]
-	[[Category: ~~Luisi, B F~~]]	+	[[Category: Bandyra KJ]]
-	[[Category: ~~Hydrolase~~]]	+	[[Category: Luisi BF]]
-	[[Category: ~~Hydrolytic mechanism]]~~	+
-	~~[[Category: Regulatory rna]]~~	+
-	~~[[Category: Ribonuclease~~]]	+

OCA at 08:21, 10 October 2018

2018-10-10T08:21:05Z

←Older revision		Revision as of 08:21, 10 October 2018
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	<StructureSection load='5f6c' size='340' side='right' caption='[[5f6c]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='5f6c' size='340' side='right' caption='[[5f6c]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5f6c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F6C FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5f6c]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F6C FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">rne, ams, hmp1, b1084, JW1071 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_E Ribonuclease E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.12 3.1.26.12] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_E Ribonuclease E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.12 3.1.26.12] </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=5f6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6c OCA], [http://pdbe.org/5f6c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6c RCSB], [http://www.ebi.ac.uk/pdbsum/5f6c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6c 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=5f6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6c OCA], [http://pdbe.org/5f6c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6c RCSB], [http://www.ebi.ac.uk/pdbsum/5f6c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6c ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.		[[http://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The endoribonuclease RNase E is a principal factor in RNA turnover and processing that helps to exercise fine control of gene expression in bacteria. While its catalytic activity can be strongly influenced by the chemical identity of the 5' end of RNA substrates, the enzyme can also cleave numerous substrates irrespective of the chemistry of their 5' ends through a mechanism that has remained largely unexplained. We report structural and functional data illuminating details of both operational modes. Our crystal structure of RNase E in complex with the sRNA RprA reveals a duplex recognition site that saddles an inter-protomer surface to help present substrates for cleavage. Our data also reveal an autoinhibitory pocket that modulates the overall activity of the ribonuclease. Taking these findings together, we propose how RNase E uses versatile modes of RNA recognition to achieve optimal activity and specificity.
		+
		+	Substrate Recognition and Autoinhibition in the Central Ribonuclease RNase E.,Bandyra KJ, Wandzik JM, Luisi BF Mol Cell. 2018 Sep 20. pii: S1097-2765(18)30699-3. doi:, 10.1016/j.molcel.2018.08.039. PMID:30270108<ref>PMID:30270108</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5f6c" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Ribonuclease E]]		[[Category: Ribonuclease E]]
	[[Category: Bandyra, K J]]		[[Category: Bandyra, K J]]

OCA at 19:13, 15 December 2016

2016-12-15T19:13:23Z

←Older revision		Revision as of 19:13, 15 December 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The ~~entry~~ 5f6c is ~~ON HOLD until Paper Publication~~	+	==The structure of E. coli RNase E catalytically inactive mutant with RNA bound==
-		+	<StructureSection load='5f6c' size='340' side='right' caption='[[5f6c]], [[Resolution\|resolution]] 3.00Å' scene=''>
-	~~Authors~~: ~~Bandyra~~, K.J., ~~Luisi~~, B.F.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5f6c]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5F6C OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5F6C FirstGlance]. <br>
-	~~Description~~: ~~The structure~~ of E. coli ~~RNase~~ E ~~catalytically inactive mutant with RNA bound~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribonuclease_E Ribonuclease E], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.26.12 3.1.26.12] </span></td></tr>
-	[[Category: Luisi, B.F]]	+	<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=5f6c FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5f6c OCA], [http://pdbe.org/5f6c PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5f6c RCSB], [http://www.ebi.ac.uk/pdbsum/5f6c PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5f6c ProSAT]</span></td></tr>
-	[[Category: ~~Bandyra, K.J~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RNE_ECOLI RNE_ECOLI]] Matures 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of colE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in E.coli. It initiates the decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly(A) tails by an endonucleolytic process.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Ribonuclease E]]
		+	[[Category: Bandyra, K J]]
		+	[[Category: Luisi, B F]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolytic mechanism]]
		+	[[Category: Regulatory rna]]
		+	[[Category: Ribonuclease]]

OCA at 10:58, 19 October 2016

2016-10-19T10:58:57Z

←Older revision		Revision as of 10:58, 19 October 2016
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5f6c is ON HOLD	+	The entry 5f6c is ON HOLD until Paper Publication

	Authors: Bandyra, K.J., Luisi, B.F.		Authors: Bandyra, K.J., Luisi, B.F.

OCA: Protected "5f6c" [edit=sysop:move=sysop]

2015-12-16T12:36:37Z

Protected "5f6c" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:36, 16 December 2015

OCA: New page: '''Unreleased structure''' The entry 5f6c is ON HOLD Authors: Bandyra, K.J., Luisi, B.F. Description: The structure of E. coli RNase E catalytically inactive mutant with RNA bound [[Ca...

2015-12-16T12:36:35Z

New page: '''Unreleased structure''' The entry 5f6c is ON HOLD Authors: Bandyra, K.J., Luisi, B.F. Description: The structure of E. coli RNase E catalytically inactive mutant with RNA bound [[Ca...

New page

'''Unreleased structure'''

The entry 5f6c is ON HOLD

Authors: Bandyra, K.J., Luisi, B.F.

Description: The structure of E. coli RNase E catalytically inactive mutant with RNA bound
[[Category: Unreleased Structures]]
[[Category: Luisi, B.F]]
[[Category: Bandyra, K.J]]