6pfq - Revision history

OCA at 14:54, 13 March 2024

OCA — Wed, 13 Mar 2024 14:54:52 GMT

←Older revision		Revision as of 14:54, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6pfq' size='340' side='right'caption='[[6pfq]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6pfq' size='340' side='right'caption='[[6pfq]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pfq]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Candida_kefyr Candida kefyr~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PFQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pfq]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_marxianus_DMKU3-1042 Kluyveromyces marxianus DMKU3-1042]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PFQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.8Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~KLMA_50491 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=1003335 Candida kefyr])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfq OCA], [~~http~~://pdbe.org/6pfq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pfq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pfq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfq 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=6pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfq OCA], [https://pdbe.org/6pfq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pfq RCSB], [https://www.ebi.ac.uk/pdbsum/6pfq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfq ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/W0TCJ5_KLUMD W0TCJ5_KLUMD]
-	U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.	+
-		+
-	Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.,Nomura Y, Montemayor EJ, Virta JM, Hayes SM, Butcher SE Nucleic Acids Res. 2020 Feb 20;48(3):~~1423-1434. doi: 10.1093~~/~~nar~~/~~gkz1177~~. ~~PMID:31832688<ref>PMID:31832688</ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.~~S. National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6pfq" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Candida kefyr~~]]	+	[[Category: Kluyveromyces marxianus DMKU3-1042]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Butcher~~, S E~~]]	+	[[Category: Butcher SE]]
-	[[Category: Montemayor~~, E J~~]]	+	[[Category: Montemayor EJ]]
-	[[Category: Nomura, Y]]	+	[[Category: Nomura Y]]
-	~~[[Category: 2h phosphodiesterase superfamily]]~~	+
-	~~[[Category: Exonuclease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: U6 snrna~~]]	+

OCA at 06:02, 20 May 2020

OCA — Wed, 20 May 2020 06:02:51 GMT

←Older revision		Revision as of 06:02, 20 May 2020
Line 3:		Line 3:
	<StructureSection load='6pfq' size='340' side='right'caption='[[6pfq]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='6pfq' size='340' side='right'caption='[[6pfq]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pfq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PFQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pfq]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Candida_kefyr Candida kefyr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PFQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfq OCA], [http://pdbe.org/6pfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pfq RCSB], [http://www.ebi.ac.uk/pdbsum/6pfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfq ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KLMA_50491 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1003335 Candida kefyr])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfq OCA], [http://pdbe.org/6pfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pfq RCSB], [http://www.ebi.ac.uk/pdbsum/6pfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfq ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.
		+
		+	Structural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.,Nomura Y, Montemayor EJ, Virta JM, Hayes SM, Butcher SE Nucleic Acids Res. 2020 Feb 20;48(3):1423-1434. doi: 10.1093/nar/gkz1177. PMID:31832688<ref>PMID:31832688</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6pfq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Candida kefyr]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Butcher, S E]]		[[Category: Butcher, S E]]

OCA at 15:11, 11 December 2019

OCA — Wed, 11 Dec 2019 15:11:11 GMT

←Older revision		Revision as of 15:11, 11 December 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6pfq ~~is ON HOLD until Paper Publication~~	+	==Structure of Kluyveromyces marxianus Usb1==
-		+	<StructureSection load='6pfq' size='340' side='right'caption='[[6pfq]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6pfq]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PFQ FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6pfq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfq OCA], [http://pdbe.org/6pfq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pfq RCSB], [http://www.ebi.ac.uk/pdbsum/6pfq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfq ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Butcher, S E]]
		+	[[Category: Montemayor, E J]]
		+	[[Category: Nomura, Y]]
		+	[[Category: 2h phosphodiesterase superfamily]]
		+	[[Category: Exonuclease]]
		+	[[Category: Hydrolase]]
		+	[[Category: U6 snrna]]

OCA at 08:56, 17 July 2019

OCA — Wed, 17 Jul 2019 08:56:55 GMT

←Older revision		Revision as of 08:56, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 03 Jul 2019 04:16:31 GMT

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

←Older revision

Revision as of 04:16, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pfq is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 03 Jul 2019 04:16:30 GMT

New page: '''Unreleased structure''' The entry 6pfq is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6pfq is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]