6r9m - Revision history

OCA at 12:17, 24 January 2024

2024-01-24T12:17:41Z

←Older revision		Revision as of 12:17, 24 January 2024
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	<StructureSection load='6r9m' size='340' side='right'caption='[[6r9m]], [[Resolution\|resolution]] 3.33Å' scene=''>		<StructureSection load='6r9m' size='340' side='right'caption='[[6r9m]], [[Resolution\|resolution]] 3.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r9m]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r9m]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R9M FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6r9i\|6r9i]]</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]] 3.329Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">PAN2, YGL094C ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=559292 Baker's yeast])</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=6r9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9m OCA], [https://pdbe.org/6r9m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r9m RCSB], [https://www.ebi.ac.uk/pdbsum/6r9m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9m ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9m OCA], [~~http~~://pdbe.org/6r9m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r9m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r9m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9m ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST]] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref>	+	[https://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hill, C H~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Passmore, L A~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Stowell, J A.W~~]]	+	[[Category: Hill CH]]
-	[[Category: ~~Tang, T T.L~~]]	+	[[Category: Passmore LA]]
-	[[Category: ~~Deadenylase~~]]	+	[[Category: Stowell JAW]]
-	[[Category: ~~Dedd rnase]]~~	+	[[Category: Tang TTL]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Pseudoubiquitin hydrolase~~]]	+

OCA at 06:44, 29 May 2019

2019-05-29T06:44:11Z

←Older revision		Revision as of 06:44, 29 May 2019
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	<StructureSection load='6r9m' size='340' side='right'caption='[[6r9m]], [[Resolution\|resolution]] 3.33Å' scene=''>		<StructureSection load='6r9m' size='340' side='right'caption='[[6r9m]], [[Resolution\|resolution]] 3.33Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r9m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r9m]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9M FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r9i\|6r9i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r9i\|6r9i]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PAN2, YGL094C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9m OCA], [http://pdbe.org/6r9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9m RCSB], [http://www.ebi.ac.uk/pdbsum/6r9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9m 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=6r9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9m OCA], [http://pdbe.org/6r9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9m RCSB], [http://www.ebi.ac.uk/pdbsum/6r9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9m ProSAT]</span></td></tr>
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST]] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref>		[[http://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST]] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The 3' poly(A) tail of messenger RNA is fundamental to regulating eukaryotic gene expression. Shortening of the poly(A) tail, termed deadenylation, reduces transcript stability and inhibits translation. Nonetheless, the mechanism for poly(A) recognition by the conserved deadenylase complexes Pan2-Pan3 and Ccr4-Not is poorly understood. Here we provide a model for poly(A) RNA recognition by two DEDD-family deadenylase enzymes, Pan2 and the Ccr4-Not nuclease Caf1. Crystal structures of Saccharomyces cerevisiae Pan2 in complex with RNA show that, surprisingly, Pan2 does not form canonical base-specific contacts. Instead, it recognizes the intrinsic stacked, helical conformation of poly(A) RNA. Using a fully reconstituted biochemical system, we show that disruption of this structure-for example, by incorporation of guanosine into poly(A)-inhibits deadenylation by both Pan2 and Caf1. Together, these data establish a paradigm for specific recognition of the conformation of poly(A) RNA by proteins that regulate gene expression.
		+
		+	The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases.,Tang TTL, Stowell JAW, Hill CH, Passmore LA Nat Struct Mol Biol. 2019 May 20. pii: 10.1038/s41594-019-0227-9. doi:, 10.1038/s41594-019-0227-9. PMID:31110294<ref>PMID:31110294</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6r9m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hill, C H]]		[[Category: Hill, C H]]

OCA at 06:59, 23 May 2019

2019-05-23T06:59:07Z

←Older revision		Revision as of 06:59, 23 May 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6r9m is ~~ON HOLD~~	+	==Structure of Saccharomyces cerevisiae apo Pan2 pseudoubiquitin hydrolase-RNA exonuclease (UCH-Exo) module in complex with AAGGAA RNA==
-		+	<StructureSection load='6r9m' size='340' side='right'caption='[[6r9m]], [[Resolution\|resolution]] 3.33Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6r9m]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R9M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R9M FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r9i\|6r9i]]</td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Poly(A)-specific_ribonuclease Poly(A)-specific ribonuclease], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.13.4 3.1.13.4] </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=6r9m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r9m OCA], [http://pdbe.org/6r9m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r9m RCSB], [http://www.ebi.ac.uk/pdbsum/6r9m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r9m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAN2_YEAST PAN2_YEAST]] Catalytic subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in mRNA turnover. PAN specifically shortens poly(A) tails of RNA when the poly(A) stretch is bound by poly(A)-binding protein PAB1, which is followed by rapid degradation of the shortened mRNA tails by the CCR4-NOT complex. Deadenylated mRNAs are then degraded by two alternative mechanisms, namely exosome-mediated 3'-5' exonucleolytic degradation, or deadenlyation-dependent mRNA decaping by DCP1-DCP2 and subsequent 5'-3' exonucleolytic degradation by XRN1. May also be involved in post-transcriptional maturation of mRNA poly(A) tails, trimming the tails from their synthesized length to the slightly shorter, apparently messenger-specific length found on newly exported mRNAs. PAN cooperates with protein kinase DUN1 in the regulation of RAD5 mRNA levels and cell survival in response to replicational stress.<ref>PMID:8550599</ref> <ref>PMID:1358757</ref> <ref>PMID:8816488</ref> <ref>PMID:9774670</ref> <ref>PMID:11239395</ref> <ref>PMID:11953437</ref> <ref>PMID:15630021</ref> <ref>PMID:15894541</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hill, C H]]
		+	[[Category: Passmore, L A]]
		+	[[Category: Stowell, J A.W]]
		+	[[Category: Tang, T T.L]]
		+	[[Category: Deadenylase]]
		+	[[Category: Dedd rnase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Pseudoubiquitin hydrolase]]

OCA: Protected "6r9m" [edit=sysop:move=sysop]

2019-04-10T05:47:00Z

Protected "6r9m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r9m is ON HOLD Authors: Description: Category: Unreleased Structures

2019-04-10T05:46:58Z

New page: '''Unreleased structure''' The entry 6r9m is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r9m is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]