5a0t - Revision history

OCA at 11:02, 10 January 2024

OCA — Wed, 10 Jan 2024 11:02:17 GMT

←Older revision		Revision as of 11:02, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A0T FirstGlance]. <br>		<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A0T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.283Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [https://pdbe.org/5a0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [https://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t 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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [https://pdbe.org/5a0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [https://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:51, 18 May 2023

OCA — Thu, 18 May 2023 07:51:19 GMT

←Older revision		Revision as of 07:51, 18 May 2023
Line 3:		Line 3:
	<StructureSection load='5a0t' size='340' side='right'caption='[[5a0t]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='5a0t' size='340' side='right'caption='[[5a0t]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Escherichia_coli~~ Escherichia coli] and [~~http~~://en.wikipedia.org/wiki/~~Strco Strco~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5A0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_BL21(DE3) Escherichia coli BL21(DE3)] and [https://en.wikipedia.org/wiki/Streptomyces_coelicolor_A3(2) Streptomyces coelicolor A3(2)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5A0T FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]~~</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [https://pdbe.org/5a0t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [https://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t 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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [~~http~~://pdbe.org/5a0t PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O86842_STRCO O86842_STRCO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 20:

	==See Also==		==See Also==
-	*[[Ribonuclease\|Ribonuclease]]	+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Strco]]~~	+	[[Category: Bralley P]]
-	[[Category: Bralley, P]]	+	[[Category: Jones GH]]
-	[[Category: Jones~~, G H~~]]	+	[[Category: Luisi BF]]
-	[[Category: Luisi~~, B F~~]]	+	[[Category: Pei XY]]
-	[[Category: Pei~~, X Y]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: Ribonuclease]]~~	+
-	~~[[Category: Rnase j~~]]	+

OCA at 07:54, 26 June 2019

OCA — Wed, 26 Jun 2019 07:54:24 GMT

←Older revision		Revision as of 07:54, 26 June 2019
Line 1:		Line 1:
		+
	==Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family==		==Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family==
-	<StructureSection load='5a0t' size='340' side='right' caption='[[5a0t]], [[Resolution\|resolution]] 2.28Å' scene=''>	+	<StructureSection load='5a0t' size='340' side='right'caption='[[5a0t]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia coli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A0T FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] and [http://en.wikipedia.org/wiki/Strco Strco]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A0T FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [http://pdbe.org/5a0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [http://www.ebi.ac.uk/pdbsum/5a0t 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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [http://pdbe.org/5a0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [http://www.ebi.ac.uk/pdbsum/5a0t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5a0t ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5a0t" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5a0t" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ribonuclease\|Ribonuclease]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
		+	[[Category: Large Structures]]
		+	[[Category: Strco]]
	[[Category: Bralley, P]]		[[Category: Bralley, P]]
	[[Category: Jones, G H]]		[[Category: Jones, G H]]

OCA at 07:26, 7 October 2015

OCA — Wed, 07 Oct 2015 07:26:21 GMT

←Older revision		Revision as of 07:26, 7 October 2015
Line 5:		Line 5:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [http://www.ebi.ac.uk/pdbsum/5a0t 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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [http://pdbe.org/5a0t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [http://www.ebi.ac.uk/pdbsum/5a0t PDBsum]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		Line 15:
	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 5a0t" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:12, 20 August 2015

OCA — Thu, 20 Aug 2015 12:12:17 GMT

←Older revision		Revision as of 12:12, 20 August 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Catalysis and 5' end sensing by ribonuclease RNase J of the metallo- beta-lactamase family==
		+	<StructureSection load='5a0t' size='340' side='right' caption='[[5a0t]], [[Resolution\|resolution]] 2.28Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5a0t]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5A0T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5A0T FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5a0v\|5a0v]]</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=5a0t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5a0t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=5a0t RCSB], [http://www.ebi.ac.uk/pdbsum/5a0t PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-beta-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 A and 2.80 A resolution, respectively. These structures reveal snapshots of the enzyme cleaving substrate directionally and sequentially from the 5' terminus. In the pre-cleavage state, a water molecule is coordinated to a zinc ion pair in the active site but is imperfectly oriented to launch a nucleophilic attack on the phosphate backbone. A conformational switch is envisaged that enables the in-line positioning of the attacking water and may be facilitated by magnesium ions. Adjacent to the scissile bond, four bases are stacked in a tightly sandwiching pocket, and mutagenesis results indicate that this organization helps to drive processive exo-ribonucleolytic cleavage. Like its numerous homologues, S. coelicolor RNase J can also cleave some RNA internally, and the structural data suggest how the preference for exo- versus endo-cleavage mode is linked with recognition of the chemical status of the substrate's 5' end.

-	~~The entry 5a0t is ON HOLD~~	+	Linkage of catalysis and 5' end recognition in ribonuclease RNase J.,Pei XY, Bralley P, Jones GH, Luisi BF Nucleic Acids Res. 2015 Aug 7. pii: gkv732. PMID:26253740<ref>PMID:26253740</ref>

-	~~Authors: Pei~~, X.Y.~~, Bralley, P., Jones, G.H., Luisi, B.F~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Catalysis and 5' end sensing by ribonuclease RNase J of the metallo-beta-lactamase family~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
-	~~[[Category: Luisi, B.F]]~~	+	__TOC__
-	[[Category: ~~Pei, X.Y~~]]	+	</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Bralley, P]]		[[Category: Bralley, P]]
-	[[Category: Jones, G.H]]	+	[[Category: Jones, G H]]
		+	[[Category: Luisi, B F]]
		+	[[Category: Pei, X Y]]
		+	[[Category: Endonuclease]]
		+	[[Category: Exonuclease]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: Ribonuclease]]
		+	[[Category: Rnase j]]

OCA: Protected "5a0t" [edit=sysop:move=sysop]

OCA — Thu, 30 Apr 2015 10:27:49 GMT

Protected "5a0t" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:27, 30 April 2015

OCA: New page: '''Unreleased structure''' The entry 5a0t is ON HOLD Authors: Pei, X.Y., Bralley, P., Jones, G.H., Luisi, B.F. Description: Catalysis and 5' end sensing by ribonuclease RNase J of the ...

OCA — Thu, 30 Apr 2015 10:27:48 GMT

New page: '''Unreleased structure''' The entry 5a0t is ON HOLD Authors: Pei, X.Y., Bralley, P., Jones, G.H., Luisi, B.F. Description: Catalysis and 5' end sensing by ribonuclease RNase J of the ...

New page

'''Unreleased structure'''

The entry 5a0t is ON HOLD

Authors: Pei, X.Y., Bralley, P., Jones, G.H., Luisi, B.F.

Description: Catalysis and 5' end sensing by ribonuclease RNase J of the metallo-beta-lactamase family
[[Category: Unreleased Structures]]
[[Category: Luisi, B.F]]
[[Category: Pei, X.Y]]
[[Category: Bralley, P]]
[[Category: Jones, G.H]]