7ug9 - Revision history

OCA at 17:15, 18 October 2023

OCA — Wed, 18 Oct 2023 17:15:51 GMT

←Older revision		Revision as of 17:15, 18 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7ug9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UG9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[7ug9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UG9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.69Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ug9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ug9 OCA], [https://pdbe.org/7ug9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ug9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ug9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ug9 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=7ug9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ug9 OCA], [https://pdbe.org/7ug9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ug9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ug9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ug9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/J7Q776_ECOLX J7Q776_ECOLX]]	+	[https://www.uniprot.org/uniprot/J7Q776_ECOLX J7Q776_ECOLX]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:58, 7 September 2022

OCA — Wed, 07 Sep 2022 18:58:07 GMT

←Older revision		Revision as of 18:58, 7 September 2022
Line 9:		Line 9:
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/J7Q776_ECOLX J7Q776_ECOLX]]		[[https://www.uniprot.org/uniprot/J7Q776_ECOLX J7Q776_ECOLX]]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Identification of metabolite caps including FAD on the 5' end of RNA has uncovered a previously unforeseen intersection between cellular metabolism and gene expression. To understand the function of FAD caps in cellular physiology, we characterised the proteins interacting with FAD caps in budding yeast. Here we demonstrate that highly conserved 5'-3' exoribonucleases, Xrn1 and Rat1, physically interact with the RNA 5' FAD cap and both possess FAD cap decapping (deFADding) activity and subsequently degrade the resulting RNA. Xrn1 deFADding activity was also evident in human cells indicating its evolutionary conservation. Furthermore, we report that the recently identified bacterial 5'-3' exoribonuclease RNase AM also possesses deFADding activity that can degrade FAD-capped RNAs in vitro and in Escherichia coli cells. To gain a molecular understanding of the deFADding reaction, an RNase AM crystal structure with three manganese ions coordinated by a sulfate molecule and the active site amino acids was generated that provided details underlying hydrolysis of the FAD cap. Our findings reveal a general propensity for 5'-3' exoribonucleases to hydrolyse and degrade RNAs with 5' end noncanonical caps in addition to their well characterized 5' monophosphate RNA substrates indicating an intrinsic property of 5'-3' exoribonucleases.
		+
		+	Identification of a novel deFADding activity in human, yeast and bacterial 5' to 3' exoribonucleases.,Sharma S, Yang J, Doamekpor SK, Grudizen-Nogalska E, Tong L, Kiledjian M Nucleic Acids Res. 2022 Aug 26;50(15):8807-8817. doi: 10.1093/nar/gkac617. PMID:35904778<ref>PMID:35904778</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ug9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:49, 7 September 2022

OCA — Wed, 07 Sep 2022 16:49:11 GMT

←Older revision		Revision as of 16:49, 7 September 2022
Line 1:		Line 1:

	==Crystal structure of RNase AM PHP domain==		==Crystal structure of RNase AM PHP domain==
-	<StructureSection load='7ug9' size='340' side='right'caption='[[7ug9]]' scene=''>	+	<StructureSection load='7ug9' size='340' side='right'caption='[[7ug9]], [[Resolution\|resolution]] 1.69Å' 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=7UG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UG9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ug9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UG9 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=7ug9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ug9 OCA], [https://pdbe.org/7ug9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ug9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ug9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ug9 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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7ug9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ug9 OCA], [https://pdbe.org/7ug9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ug9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ug9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ug9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/J7Q776_ECOLX J7Q776_ECOLX]]
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Doamekpor SK]]		[[Category: Doamekpor SK]]
	[[Category: Tong L]]		[[Category: Tong L]]

OCA at 06:37, 31 August 2022

OCA — Wed, 31 Aug 2022 06:37:21 GMT

←Older revision		Revision as of 06:37, 31 August 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7ug9 ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of RNase AM PHP domain==
-		+	<StructureSection load='7ug9' size='340' side='right'caption='[[7ug9]]' scene=''>
-	~~Authors~~: ~~Doamekpor~~, S.K., ~~Tong~~, L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7UG9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7UG9 FirstGlance]. <br>
-	~~Description: Crystal structure of RNase AM PHP domain~~	+	</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=7ug9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ug9 OCA], [https://pdbe.org/7ug9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ug9 RCSB], [https://www.ebi.ac.uk/pdbsum/7ug9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ug9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Tong, L~~]]	+	__TOC__
-	[[Category: ~~Doamekpor, S.K~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Doamekpor SK]]
		+	[[Category: Tong L]]

OCA at 10:24, 27 April 2022

OCA — Wed, 27 Apr 2022 10:24:14 GMT

←Older revision		Revision as of 10:24, 27 April 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ug9 is ON HOLD	+	The entry 7ug9 is ON HOLD until Paper Publication

	Authors: Doamekpor, S.K., Tong, L.		Authors: Doamekpor, S.K., Tong, L.

OCA: Protected "7ug9" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2022 09:36:50 GMT

Protected "7ug9" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:36, 30 March 2022

OCA: New page: '''Unreleased structure''' The entry 7ug9 is ON HOLD Authors: Doamekpor, S.K., Tong, L. Description: Crystal structure of RNase AM PHP domain Category: Unreleased Structures [[Cate...

OCA — Wed, 30 Mar 2022 09:36:49 GMT

New page: '''Unreleased structure''' The entry 7ug9 is ON HOLD Authors: Doamekpor, S.K., Tong, L. Description: Crystal structure of RNase AM PHP domain Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 7ug9 is ON HOLD

Authors: Doamekpor, S.K., Tong, L.

Description: Crystal structure of RNase AM PHP domain
[[Category: Unreleased Structures]]
[[Category: Tong, L]]
[[Category: Doamekpor, S.K]]