2lli - Revision history

OCA at 05:45, 15 May 2024

2024-05-15T05:45:42Z

← Older revision		Revision as of 05:45, 15 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [https://pdbe.org/2lli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [https://www.ebi.ac.uk/pdbsum/2lli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli 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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [https://pdbe.org/2lli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [https://www.ebi.ac.uk/pdbsum/2lli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:06, 15 February 2023

2023-02-15T11:06:34Z

← Older revision		Revision as of 11:06, 15 February 2023
Line 1:		Line 1:

	==Low resolution structure of RNA-binding subunit of the TRAMP complex==		==Low resolution structure of RNA-binding subunit of the TRAMP complex==
	<StructureSection load='2lli' size='340' side='right'caption='[[2lli~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>		<StructureSection load='2lli' size='340' side='right'caption='[[2lli]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([https://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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [https://pdbe.org/2lli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [https://www.ebi.ac.uk/pdbsum/2lli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli 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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [https://pdbe.org/2lli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [https://www.ebi.ac.uk/pdbsum/2lli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/AIR2_YEAST AIR2_YEAST]] Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1.<ref>PMID:10896665</ref> <ref>PMID:15935758</ref> <ref>PMID:15935759</ref> <ref>PMID:15828860</ref> <ref>PMID:20696927</ref>		[https://www.uniprot.org/uniprot/AIR2_YEAST AIR2_YEAST] Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1.<ref>PMID:10896665</ref> <ref>PMID:15935758</ref> <ref>PMID:15935759</ref> <ref>PMID:15828860</ref> <ref>PMID:20696927</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: Arce~~, M S~~]]		[[Category: Saccharomyces cerevisiae S288C]]
	[[Category: Cerna, H]]		[[Category: Arce MS]]
	[[Category: Holub, P]]		[[Category: Cerna H]]
	[[Category: Hrazdilova, K]]		[[Category: Holub P]]
	[[Category: Lalakova, J]]		[[Category: Hrazdilova K]]
	[[Category: Pasulka, J]]		[[Category: Lalakova J]]
	[[Category: Sarazova, M]]		[[Category: Pasulka J]]
	[[Category: Stefl, R]]		[[Category: Sarazova M]]
	[[Category: Vanacova, S]]		[[Category: Stefl R]]
	~~[[Category: Exosome]]~~		[[Category: Vanacova S]]
	~~[[Category: Rna binding]]~~
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Rna degradation]]~~
	~~[[Category: Rna surveillance~~]]

OCA at 10:13, 12 May 2021

2021-05-12T10:13:03Z

← Older revision		Revision as of 10:13, 12 May 2021
Line 1:		Line 1:

	==Low resolution structure of RNA-binding subunit of the TRAMP complex==		==Low resolution structure of RNA-binding subunit of the TRAMP complex==
	<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lli' size='340' side='right'caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2LLI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2LLI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([https://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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [~~http~~://pdbe.org/2lli PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2lli PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli 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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [https://pdbe.org/2lli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [https://www.ebi.ac.uk/pdbsum/2lli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/AIR2_YEAST AIR2_YEAST]] Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1.<ref>PMID:10896665</ref> <ref>PMID:15935758</ref> <ref>PMID:15935759</ref> <ref>PMID:15828860</ref> <ref>PMID:20696927</ref>		[[https://www.uniprot.org/uniprot/AIR2_YEAST AIR2_YEAST]] Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1.<ref>PMID:10896665</ref> <ref>PMID:15935758</ref> <ref>PMID:15935759</ref> <ref>PMID:15828860</ref> <ref>PMID:20696927</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
			[[Category: Large Structures]]
	[[Category: Arce, M S]]		[[Category: Arce, M S]]
	[[Category: Cerna, H]]		[[Category: Cerna, H]]

OCA at 19:59, 1 August 2018

2018-08-01T19:59:15Z

← Older revision		Revision as of 19:59, 1 August 2018
Line 1:		Line 1:

	==Low resolution structure of RNA-binding subunit of the TRAMP complex==		==Low resolution structure of RNA-binding subunit of the TRAMP complex==
	<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://pdbe.org/2lli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://pdbe.org/2lli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2lli ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:26, 10 September 2015

2015-09-10T20:26:14Z

← Older revision		Revision as of 20:26, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LLI FirstGlance]. <br>		<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LLI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~4932 Saccharomyces cerevisiae~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://pdbe.org/2lli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 2lli" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Baker's yeast]]
	[[Category: Arce, M S]]		[[Category: Arce, M S]]
	[[Category: Cerna, H]]		[[Category: Cerna, H]]

OCA at 05:42, 25 December 2014

2014-12-25T05:42:10Z

← Older revision		Revision as of 05:42, 25 December 2014
Line 7:		Line 7:
	<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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/AIR2_YEAST AIR2_YEAST]] Component of the TRAMP (TRF4) complex which has a poly(A) RNA polymerase activity and is involved in a post-transcriptional quality control mechanism limiting inappropriate expression of genetic information. Polyadenylation is required for the degradative activity of the exosome on several of its nuclear RNA substrates like cryptic transcripts generated by RNA polymerase II and III, or hypomethylated pre-tRNAi-Met. Both complexes polyadenylate RNA processing and degradation intermediates of snRNAs, snoRNAs and mRNAs that accumulate in strains lacking a functional exosome. AIR2 also inhibits the methylation of NPL3 mediated by HMT1 through its interaction with HMT1.<ref>PMID:10896665</ref> <ref>PMID:15935758</ref> <ref>PMID:15935759</ref> <ref>PMID:15828860</ref> <ref>PMID:20696927</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 06:43, 22 December 2014

2014-12-22T06:43:33Z

← Older revision		Revision as of 06:43, 22 December 2014
Line 2:		Line 2:
	<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. <br>		<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2LLI FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
	<tr~~><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class~~='~~plainlinks~~'~~>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </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=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</span></td></tr>
	~~<tr~~><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</span></td></tr>		</table>
	<table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 13:
	Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.,Holub P, Lalakova J, Cerna H, Pasulka J, Sarazova M, Hrazdilova K, Arce MS, Hobor F, Stefl R, Vanacova S Nucleic Acids Res. 2012 Mar 8. PMID:22402490<ref>PMID:22402490</ref>		Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.,Holub P, Lalakova J, Cerna H, Pasulka J, Sarazova M, Hrazdilova K, Arce MS, Hobor F, Stefl R, Vanacova S Nucleic Acids Res. 2012 Mar 8. PMID:22402490<ref>PMID:22402490</ref>

	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 21:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Arce, M S.]]		[[Category: Arce, M S]]
	[[Category: Cerna, H.]]		[[Category: Cerna, H]]
	[[Category: Holub, P.]]		[[Category: Holub, P]]
	[[Category: Hrazdilova, K.]]		[[Category: Hrazdilova, K]]
	[[Category: Lalakova, J.]]		[[Category: Lalakova, J]]
	[[Category: Pasulka, J.]]		[[Category: Pasulka, J]]
	[[Category: Sarazova, M.]]		[[Category: Sarazova, M]]
	[[Category: Stefl, R.]]		[[Category: Stefl, R]]
	[[Category: Vanacova, S.]]		[[Category: Vanacova, S]]
	[[Category: Exosome]]		[[Category: Exosome]]
	[[Category: Rna binding]]		[[Category: Rna binding]]

OCA at 07:47, 14 May 2014

2014-05-14T07:47:38Z

← Older revision		Revision as of 07:47, 14 May 2014
Line 1:		Line 1:
	[[~~Image~~:~~2lli~~.~~png~~\|~~left~~\|~~200px~~]]		==Low resolution structure of RNA-binding subunit of the TRAMP complex==
			<StructureSection load='2lli' size='340' side='right' caption='[[2lli]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2lli]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">AIR2, YDL175C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2lli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2lli OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2lli RCSB], [http://www.ebi.ac.uk/pdbsum/2lli PDBsum]</span></td></tr>
			<table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Trf4/5p-Air1/2p-Mtr4p polyadenylation complex (TRAMP) is an essential component of nuclear RNA surveillance in yeast. It recognizes a variety of nuclear transcripts produced by all three RNA polymerases, adds short poly(A) tails to aberrant or unstable RNAs and activates the exosome for their degradation. Despite the advances in understanding the structural features of the isolated complex subunits or their fragments, the details of complex assembly, RNA recognition and exosome activation remain poorly understood. Here we provide the first understanding of the RNA binding mode of the complex. We show that Air2p is an RNA-binding subunit of TRAMP. We identify the zinc knuckles (ZnK) 2, 3 and 4 as the RNA-binding domains, and reveal the essentiality of ZnK4 for TRAMP4 polyadenylation activity. Furthermore, we identify Air2p as the key component of TRAMP4 assembly providing bridging between Mtr4p and Trf4p. The former is bound via the N-terminus of Air2p, while the latter is bound via ZnK5, the linker between ZnK4 and 5 and the C-terminus of the protein. Finally, we uncover the RNA binding part of the Mtr4p arch, the KOW domain, as the essential component for TRAMP-mediated exosome activation.

	~~{{STRUCTURE_2lli\| PDB=2lli \| SCENE= }}~~		Air2p is critical for the assembly and RNA-binding of the TRAMP complex and the KOW domain of Mtr4p is crucial for exosome activation.,Holub P, Lalakova J, Cerna H, Pasulka J, Sarazova M, Hrazdilova K, Arce MS, Hobor F, Stefl R, Vanacova S Nucleic Acids Res. 2012 Mar 8. PMID:22402490<ref>PMID:22402490</ref>

	~~===Low resolution structure of RNA-binding subunit~~ of the ~~TRAMP complex===~~		From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_22402490}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2lli]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full experimental information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2LLI OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:022402490<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Arce, M S.]]		[[Category: Arce, M S.]]

OCA at 07:23, 11 July 2012

2012-07-11T07:23:05Z

← Older revision		Revision as of 07:23, 11 July 2012
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	[[Image:2lli.~~jpg~~\|left\|200px]]		[[Image:2lli.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2lli", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2lli\| PDB=2lli \| SCENE= }}		{{STRUCTURE_2lli\| PDB=2lli \| SCENE= }}

	===Low resolution structure of RNA-binding subunit of the TRAMP complex===		===Low resolution structure of RNA-binding subunit of the TRAMP complex===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_22402490}}, adds the Publication Abstract to the page~~
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	{{ABSTRACT_PUBMED_22402490}}		{{ABSTRACT_PUBMED_22402490}}

OCA at 07:35, 21 March 2012

2012-03-21T07:35:54Z

@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
+[[Image:2lli.jpg|left|200px]]
-The entry 2lli is ON HOLD  until Paper Publication
+<!--
-Authors: Holub, P., Lalakova, J., Cerna, H., Sarazova, M., Pasulka, J., Hrazdilova, K., Arce, M.S., Stefl, R., Vanacova, S.
+===Low resolution structure of RNA-binding subunit of the TRAMP complex===
-Description: Low resolution structure of RNA-binding subunit of the TRAMP complex