6n6d - Revision history

OCA at 06:46, 11 October 2023

OCA — Wed, 11 Oct 2023 06:46:26 GMT

←Older revision		Revision as of 06:46, 11 October 2023
Line 3:		Line 3:
	<StructureSection load='6n6d' size='340' side='right'caption='[[6n6d]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='6n6d' size='340' side='right'caption='[[6n6d]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6d]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6D OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N6D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6d]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae] 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=6N6D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6N6D FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><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]] 1.534Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>orn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~666~~ "~~Bacillo virgola del Koch~~" ~~Trevisan 1884])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=6n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6d OCA], [~~http~~://pdbe.org/6n6d PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6n6d RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6n6d PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6d 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=6n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6d OCA], [https://pdbe.org/6n6d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6n6d RCSB], [https://www.ebi.ac.uk/pdbsum/6n6d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A0H6V4D7_VIBCL A0A0H6V4D7_VIBCL]~~] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045~~][SAAS:SAAS00859727~~]	+	[https://www.uniprot.org/uniprot/ORN_VIBCH ORN_VIBCH] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045]
	<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 6n6d" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n6d" 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: Bacillo virgola del koch trevisan 1884]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lormand, J D~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Sondermann, H~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: ~~3'-5' exoribonuclease~~]]	+	[[Category: Lormand JD]]
-	[[Category: ~~Rna binding protein]]~~	+	[[Category: Sondermann H]]
-	~~[[Category: Rna binding protein-rna complex~~]]	+

OCA at 07:23, 16 October 2019

OCA — Wed, 16 Oct 2019 07:23:10 GMT

←Older revision		Revision as of 07:23, 16 October 2019
Line 3:		Line 3:
	<StructureSection load='6n6d' size='340' side='right'caption='[[6n6d]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='6n6d' size='340' side='right'caption='[[6n6d]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n6d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6D FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n6d]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6D FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">orn ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=6n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6d OCA], [http://pdbe.org/6n6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6d RCSB], [http://www.ebi.ac.uk/pdbsum/6n6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6d 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=6n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6d OCA], [http://pdbe.org/6n6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6d RCSB], [http://www.ebi.ac.uk/pdbsum/6n6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6d ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/A0A0H6V4D7_VIBCL A0A0H6V4D7_VIBCL]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045][SAAS:SAAS00859727]		[[http://www.uniprot.org/uniprot/A0A0H6V4D7_VIBCL A0A0H6V4D7_VIBCL]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045][SAAS:SAAS00859727]
		+	<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 6n6d" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lormand, J D]]		[[Category: Lormand, J D]]

OCA at 05:39, 12 June 2019

OCA — Wed, 12 Jun 2019 05:39:30 GMT

←Older revision		Revision as of 05:39, 12 June 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n6d is ~~ON HOLD until Paper Publication~~	+	==Vibrio cholerae Oligoribonuclease bound to pAG==
-		+	<StructureSection load='6n6d' size='340' side='right'caption='[[6n6d]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6n6d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N6D OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N6D FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=6n6d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n6d OCA], [http://pdbe.org/6n6d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n6d RCSB], [http://www.ebi.ac.uk/pdbsum/6n6d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n6d ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A0H6V4D7_VIBCL A0A0H6V4D7_VIBCL]] 3'-to-5' exoribonuclease specific for small oligoribonucleotides.[HAMAP-Rule:MF_00045][SAAS:SAAS00859727]
		+	__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

OCA — Wed, 12 Dec 2018 05:20:09 GMT

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

-	The entry 6n6d is ON HOLD	+	The entry 6n6d 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 "6n6d" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:16:43 GMT

Protected "6n6d" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:16, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n6d is ON HOLD Authors: Lormand, J.D., Sondermann, H. Description: TBA Category: Unreleased Structures Category: Sondermann, H [[Category:...

OCA — Wed, 05 Dec 2018 05:16:42 GMT

New page: '''Unreleased structure''' The entry 6n6d is ON HOLD Authors: Lormand, J.D., Sondermann, H. Description: TBA Category: Unreleased Structures Category: Sondermann, H [[Category:...

New page

'''Unreleased structure'''

The entry 6n6d is ON HOLD

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

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