6n6j - Revision history

OCA at 06:46, 11 October 2023

2023-10-11T06:46:50Z

←Older revision		Revision as of 06:46, 11 October 2023
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	<StructureSection load='6n6j' size='340' side='right'caption='[[6n6j]], [[Resolution\|resolution]] 1.32Å' scene=''>		<StructureSection load='6n6j' size='340' side='right'caption='[[6n6j]], [[Resolution\|resolution]] 1.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6j]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N6J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.317Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REXO2, SFN, SMFN, CGI-114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6n6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6j OCA], [~~http~~://pdbe.org/6n6j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n6j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n6j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6j 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=6n6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6j OCA], [https://pdbe.org/6n6j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n6j RCSB], [https://www.ebi.ac.uk/pdbsum/6n6j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ORN_HUMAN ORN_HUMAN]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.<ref>PMID:23741365</ref>	+	[https://www.uniprot.org/uniprot/ORN_HUMAN ORN_HUMAN] 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.<ref>PMID:23741365</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6n6j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n6j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Exonuclease 3D structures\|Exonuclease 3D structures]]
		+	*[[Ribonuclease 3D structures\|Ribonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lormand, J D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Sondermann, H~~]]	+	[[Category: Lormand JD]]
-	[[Category: ~~3'-5' exoribonuclease]]~~	+	[[Category: Sondermann H]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna binding protein-rna complex~~]]	+

OCA at 07:24, 16 October 2019

2019-10-16T07:24:41Z

←Older revision		Revision as of 07:24, 16 October 2019
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	<StructureSection load='6n6j' size='340' side='right'caption='[[6n6j]], [[Resolution\|resolution]] 1.32Å' scene=''>		<StructureSection load='6n6j' size='340' side='right'caption='[[6n6j]], [[Resolution\|resolution]] 1.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6j]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">REXO2, SFN, SMFN, CGI-114 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6n6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6j OCA], [http://pdbe.org/6n6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6j RCSB], [http://www.ebi.ac.uk/pdbsum/6n6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6j 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=6n6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6j OCA], [http://pdbe.org/6n6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6j RCSB], [http://www.ebi.ac.uk/pdbsum/6n6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ORN_HUMAN ORN_HUMAN]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.<ref>PMID:23741365</ref>		[[http://www.uniprot.org/uniprot/ORN_HUMAN ORN_HUMAN]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.<ref>PMID:23741365</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Degradation of RNA polymers, an ubiquitous process in all cells, is catalyzed by specific subsets of endo- and exoribonucleases that together recycle RNA fragments into nucleotide monophosphate. In gamma-proteobacteria, 3-'5' exoribonucleases comprise up to eight distinct enzymes. Among them, Oligoribonuclease (Orn) is unique as its activity is required for clearing short RNA fragments, which is important for cellular fitness. However, the molecular basis of Orn's unique cellular function remained unclear. Here, we show that Orn exhibits exquisite substrate preference for diribonucleotides. Crystal structures of substrate-bound Orn reveal an active site optimized for diribonucleotides. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, Orn is the one and only diribonucleotidase that completes the terminal step of RNA degradation. Together, our studies indicate RNA degradation as a step-wise process with a dedicated enzyme for the clearance of a specific intermediate pool, diribonucleotides, that affects cellular physiology and viability.
		+
		+	A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.,Kim SK, Lormand JD, Weiss CA, Eger KA, Turdiev H, Turdiev A, Winkler WC, Sondermann H, Lee VT Elife. 2019 Jun 21;8. pii: 46313. doi: 10.7554/eLife.46313. PMID:31225796<ref>PMID:31225796</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6n6j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lormand, J D]]		[[Category: Lormand, J D]]

OCA at 05:39, 12 June 2019

2019-06-12T05:39:52Z

←Older revision		Revision as of 05:39, 12 June 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6n6j is ~~ON HOLD until Paper Publication~~	+	==Human REXO2 bound to pAA==
-		+	<StructureSection load='6n6j' size='340' side='right'caption='[[6n6j]], [[Resolution\|resolution]] 1.32Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n6j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6J FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MLI:MALONATE+ION'>MLI</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6n6j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6j OCA], [http://pdbe.org/6n6j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6j RCSB], [http://www.ebi.ac.uk/pdbsum/6n6j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6j ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ORN_HUMAN ORN_HUMAN]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides. Active on small (primarily </=5 nucleotides in length) single-stranded RNA and DNA oligomers. May have a role in cellular nucleotide recycling.<ref>PMID:23741365</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lormand, J D]]
		+	[[Category: Sondermann, H]]
		+	[[Category: 3'-5' exoribonuclease]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna binding protein-rna complex]]

OCA at 05:20, 12 December 2018

2018-12-12T05:20:29Z

←Older revision		Revision as of 05:20, 12 December 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6n6j is ON HOLD	+	The entry 6n6j is ON HOLD until Paper Publication

-	Authors: ~~Lormand, J.D., Sondermann, H.~~	+	Authors:

-	Description: ~~TBA~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sondermann, H]]
-	[[Category: Lormand, J.D]]

OCA: Protected "6n6j" [edit=sysop:move=sysop]

2018-12-05T05:17:00Z

Protected "6n6j" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:17, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n6j is ON HOLD Authors: Lormand, J.D., Sondermann, H. Description: TBA Category: Unreleased Structures Category: Sondermann, H [[Category:...

2018-12-05T05:16:58Z

New page: '''Unreleased structure''' The entry 6n6j is ON HOLD Authors: Lormand, J.D., Sondermann, H. Description: TBA Category: Unreleased Structures Category: Sondermann, H [[Category:...

New page

'''Unreleased structure'''

The entry 6n6j is ON HOLD

Authors: Lormand, J.D., Sondermann, H.

Description: TBA
[[Category: Unreleased Structures]]
[[Category: Sondermann, H]]
[[Category: Lormand, J.D]]