7opk - Revision history

OCA at 12:54, 1 February 2024

OCA — Thu, 01 Feb 2024 12:54:13 GMT

←Older revision		Revision as of 12:54, 1 February 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7opk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OPK FirstGlance]. <br>		<table><tr><td colspan='2'>[[7opk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OPK FirstGlance]. <br>
-	</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></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]] 3Å</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></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=7opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7opk OCA], [https://pdbe.org/7opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7opk RCSB], [https://www.ebi.ac.uk/pdbsum/7opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7opk 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=7opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7opk OCA], [https://pdbe.org/7opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7opk RCSB], [https://www.ebi.ac.uk/pdbsum/7opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7opk ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/G0S058_CHATD G0S058_CHATD]] Possesses 5'->3' exoribonuclease activity. May promote termination of transcription by RNA polymerase II.[PIRNR:PIRNR037239] Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.[ARBA:ARBA00025537]	+	[https://www.uniprot.org/uniprot/G0S058_CHATD G0S058_CHATD] Possesses 5'->3' exoribonuclease activity. May promote termination of transcription by RNA polymerase II.[PIRNR:PIRNR037239] Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.[ARBA:ARBA00025537]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:55, 7 September 2022

OCA — Wed, 07 Sep 2022 18:55:57 GMT

←Older revision		Revision as of 18:55, 7 September 2022
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	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/G0S058_CHATD G0S058_CHATD]] Possesses 5'->3' exoribonuclease activity. May promote termination of transcription by RNA polymerase II.[PIRNR:PIRNR037239] Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.[ARBA:ARBA00025537]		[[https://www.uniprot.org/uniprot/G0S058_CHATD G0S058_CHATD]] Possesses 5'->3' exoribonuclease activity. May promote termination of transcription by RNA polymerase II.[PIRNR:PIRNR037239] Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.[ARBA:ARBA00025537]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Nuclear magnetic resonance (NMR) methods that quantitatively probe motions on molecular and atomic levels have propelled the understanding of biomolecular processes for which static structures cannot provide a satisfactory description. In this work, we studied the structure and dynamics of the essential 100-kDa eukaryotic 5'-->3' exoribonuclease Xrn2. A combination of complementary fluorine and methyl-TROSY NMR spectroscopy reveals that the apo enzyme is highly dynamic around the catalytic center. These observed dynamics are in agreement with a transition of the enzyme from the ground state into a catalytically competent state. We show that the conformational equilibrium in Xrn2 shifts substantially toward the active state in the presence of substrate and magnesium. Finally, our data reveal that the dynamics in Xrn2 correlate with the RNA degradation rate, as a mutation that attenuates motions also affects catalytic activity. In that light, our results stress the importance of studies that go beyond static structural information.
		+
		+	Observation of conformational changes that underlie the catalytic cycle of Xrn2.,Overbeck JH, Stelzig D, Fuchs AL, Wurm JP, Sprangers R Nat Chem Biol. 2022 Aug 25. pii: 10.1038/s41589-022-01111-6. doi:, 10.1038/s41589-022-01111-6. PMID:36008487<ref>PMID:36008487</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7opk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:47, 7 September 2022

OCA — Wed, 07 Sep 2022 16:47:53 GMT

←Older revision		Revision as of 16:47, 7 September 2022
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-	==~~RNA degradation enzyme~~==	+	==Crystal structure of C. thermophilum Xrn2==
-	<StructureSection load='7opk' size='340' side='right'caption='[[7opk]]' scene=''>	+	<StructureSection load='7opk' size='340' side='right'caption='[[7opk]], [[Resolution\|resolution]] 3.00Å' 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=7OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OPK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7opk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OPK 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=7opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7opk OCA], [https://pdbe.org/7opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7opk RCSB], [https://www.ebi.ac.uk/pdbsum/7opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7opk ProSAT]</span></td></tr>	+	</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></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=7opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7opk OCA], [https://pdbe.org/7opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7opk RCSB], [https://www.ebi.ac.uk/pdbsum/7opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7opk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/G0S058_CHATD G0S058_CHATD]] Possesses 5'->3' exoribonuclease activity. May promote termination of transcription by RNA polymerase II.[PIRNR:PIRNR037239] Possesses 5'->3' exoribonuclease activity. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.[ARBA:ARBA00025537]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chaetomium thermophilum var. thermophilum DSM 1495]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Overbeck JH]]		[[Category: Overbeck JH]]
	[[Category: Sprangers R]]		[[Category: Sprangers R]]

OCA at 16:12, 6 July 2022

OCA — Wed, 06 Jul 2022 16:12:19 GMT

←Older revision		Revision as of 16:12, 6 July 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7opk ~~is ON HOLD until Paper Publication~~	+	==RNA degradation enzyme==
-		+	<StructureSection load='7opk' size='340' side='right'caption='[[7opk]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OPK FirstGlance]. <br>
-	~~Description~~:	+	</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=7opk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7opk OCA], [https://pdbe.org/7opk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7opk RCSB], [https://www.ebi.ac.uk/pdbsum/7opk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7opk ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Overbeck JH]]
		+	[[Category: Sprangers R]]

OCA at 02:33, 2 July 2021

OCA — Fri, 02 Jul 2021 02:33:00 GMT

←Older revision		Revision as of 02:33, 2 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 09 Jun 2021 11:14:45 GMT

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

←Older revision

Revision as of 11:14, 9 June 2021

OCA: New page: '''Unreleased structure''' The entry 7opk is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 Jun 2021 11:14:44 GMT

New page: '''Unreleased structure''' The entry 7opk is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7opk is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]