2jvb - Revision history

OCA at 19:06, 29 May 2024

2024-05-29T19:06:13Z

← Older revision		Revision as of 19:06, 29 May 2024
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	==Solution Structure of Catalytic Domain of yDcp2==		==Solution Structure of Catalytic Domain of yDcp2==
	<StructureSection load='2jvb' size='340' side='right'caption='[[2jvb~~]], [[NMR_Ensembles_of_Models \| 10 NMR models~~]]' scene=''>		<StructureSection load='2jvb' size='340' side='right'caption='[[2jvb]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>DCP2, PSU1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~4932 ATCC 18824])~~</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [https://pdbe.org/2jvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [https://www.ebi.ac.uk/pdbsum/2jvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jvb 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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [https://pdbe.org/2jvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [https://www.ebi.ac.uk/pdbsum/2jvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>		[https://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Atcc 18824]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Deshmukh, M~~]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: ~~Gross, J~~]]		[[Category: Deshmukh M]]
	[[Category: ~~Cytoplasm]]~~		[[Category: Gross J]]
	~~[[Category: Dcp2]]~~
	~~[[Category: Decapping]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Manganese]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Mrna decay]]~~
	~~[[Category: Mrna processing]]~~
	~~[[Category: Nonsense-mediated mrna decay]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Phosphorylation]]~~
	~~[[Category: Rna-binding~~]]

OCA at 07:58, 7 April 2021

2021-04-07T07:58:52Z

← Older revision		Revision as of 07:58, 7 April 2021
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	==Solution Structure of Catalytic Domain of yDcp2==		==Solution Structure of Catalytic Domain of yDcp2==
	<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2jvb' size='340' side='right'caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2JVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [~~http~~://pdbe.org/2jvb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2jvb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2jvb 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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [https://pdbe.org/2jvb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [https://www.ebi.ac.uk/pdbsum/2jvb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>		[[https://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
			[[Category: Large Structures]]
	[[Category: Deshmukh, M]]		[[Category: Deshmukh, M]]
	[[Category: Gross, J]]		[[Category: Gross, J]]

OCA at 10:29, 18 July 2018

2018-07-18T10:29:11Z

← Older revision		Revision as of 10:29, 18 July 2018
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	==Solution Structure of Catalytic Domain of yDcp2==		==Solution Structure of Catalytic Domain of yDcp2==
	<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
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	<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://pdbe.org/2jvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb 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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://pdbe.org/2jvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2jvb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/2jvb_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/2jvb_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jvb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Deshmukh, M]]		[[Category: Deshmukh, M]]
	[[Category: Gross, J]]		[[Category: Gross, J]]
			[[Category: Cytoplasm]]
	[[Category: Dcp2]]		[[Category: Dcp2]]
	[[Category: Decapping]]		[[Category: Decapping]]

OCA at 15:11, 11 September 2015

2015-09-11T15:11:05Z

← Older revision		Revision as of 15:11, 11 September 2015
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	<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>		<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jvb]] 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=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jvb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb 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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://pdbe.org/2jvb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2jvb" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Saccharomyces cerevisiae~~]]		[[Category: Atcc 18824]]
	[[Category: Deshmukh, M]]		[[Category: Deshmukh, M]]
	[[Category: Gross, J]]		[[Category: Gross, J]]

OCA at 18:12, 25 December 2014

2014-12-25T18:12:39Z

← Older revision		Revision as of 18:12, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2jvb]] 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=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>		<table><tr><td colspan='2'>[[2jvb]] 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=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>		</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb 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=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/DCP2_YEAST DCP2_YEAST]] Catalytic component of the decapping complex necessary for the degradation of mRNAs, both in normal mRNA turnover and in nonsense-mediated mRNA decay. Removes the 7-methyl guanine cap structure from mRNA molecules, yielding a 5'-phosphorylated mRNA fragment and 7m-GDP. Decapping is the major pathway of mRNA degradation in yeast. It occurs through deadenylation, decapping and subsequent 5' to 3' exonucleolytic decay of the transcript body.<ref>PMID:10508173</ref> <ref>PMID:11139489</ref> <ref>PMID:11741542</ref> <ref>PMID:12554866</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Deshmukh, M.]]		[[Category: Deshmukh, M]]
	[[Category: Gross, J.]]		[[Category: Gross, J]]
	[[Category: Dcp2]]		[[Category: Dcp2]]
	[[Category: Decapping]]		[[Category: Decapping]]

OCA at 09:23, 30 September 2014

2014-09-30T09:23:28Z

← Older revision		Revision as of 09:23, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2jvb~~.~~png~~\|~~left~~\|~~200px~~]]		==Solution Structure of Catalytic Domain of yDcp2==
			<StructureSection load='2jvb' size='340' side='right' caption='[[2jvb]], [[NMR_Ensembles_of_Models \| 10 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2jvb]] 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=2JVB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2JVB FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DCP2, PSU1 ([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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2jvb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jvb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2jvb RCSB], [http://www.ebi.ac.uk/pdbsum/2jvb PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jv/2jvb_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Cap hydrolysis by Dcp2 is a critical step in several eukaryotic mRNA decay pathways. Processing requires access to cap-proximal nucleotides and the coordinated assembly of a decapping mRNP, but the mechanism of substrate recognition and regulation by protein interactions have remained elusive. Using NMR spectroscopy and kinetic analyses, we show that yeast Dcp2 resolves interactions with the cap and RNA body using a bipartite surface that forms a channel intersecting the catalytic and regulatory Dcp1-binding domains. The interaction with cap is weak but specific and requires binding of the RNA body to a dynamic interface. The catalytic step is stimulated by Dcp1 and its interaction domain, likely through a substrate-induced conformational change. Thus, activation of the decapping mRNP is restricted by access to 5'-proximal nucleotides, a feature that could act as a checkpoint in mRNA metabolism.

	~~{{STRUCTURE_2jvb\| PDB=2jvb \| SCENE= }}~~		mRNA decapping is promoted by an RNA-binding channel in Dcp2.,Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross JD Mol Cell. 2008 Feb 15;29(3):324-36. PMID:18280238<ref>PMID:18280238</ref>

	~~===Solution Structure of Catalytic Domain~~ of ~~yDcp2===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18280238}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2jvb]] 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=2JVB OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:018280238<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Deshmukh, M.]]		[[Category: Deshmukh, M.]]

OCA: Protected "2jvb" [edit=sysop:move=sysop]

2013-01-07T14:17:31Z

Protected "2jvb" [edit=sysop:move=sysop]

← Older revision	Revision as of 14:17, 7 January 2013
(No difference)

OCA at 14:17, 7 January 2013

2013-01-07T14:17:29Z

← Older revision		Revision as of 14:17, 7 January 2013
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	~~{{Seed}}~~
	[[Image:2jvb.png\|left\|200px]]		[[Image:2jvb.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2jvb", 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_2jvb\| PDB=2jvb \| SCENE= }}		{{STRUCTURE_2jvb\| PDB=2jvb \| SCENE= }}

	===Solution Structure of Catalytic Domain of yDcp2===		===Solution Structure of Catalytic Domain of yDcp2===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18280238}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18280238 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18280238}}		{{ABSTRACT_PUBMED_18280238}}

	==About this Structure==		==About this Structure==
	~~2JVB~~ is a 1 chain structure of 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=2JVB OCA].		[[2jvb]] 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=2JVB OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18280238~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018280238</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Deshmukh, M.]]		[[Category: Deshmukh, M.]]
	[[Category: Gross, J.]]		[[Category: Gross, J.]]
	~~[[Category: Cytoplasm]]~~
	[[Category: Dcp2]]		[[Category: Dcp2]]
	[[Category: Decapping]]		[[Category: Decapping]]
Line 39:		Line 26:
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:37:44 2009''~~

OCA at 23:37, 17 February 2009

2009-02-17T23:37:49Z

← Older revision		Revision as of 23:37, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	2JVB is a ~~[[Single protein]]~~ structure of 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=2JVB OCA].		2JVB is a 1 chain structure of 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=2JVB OCA].

	==Reference==		==Reference==
	mRNA Decapping Is Promoted by an RNA-Binding Channel in Dcp2., Deshmukh MV, Jones BN, Quang-Dang DU, Flinders J, Floor SN, Kim C, Jemielity J, Kalek M, Darzynkiewicz E, Gross JD, Mol Cell. 2008 Feb 15;29(3):324-36. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18280238 18280238]~~		<ref group="xtra">PMID:18280238</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	~~[[Category: Single protein]]~~
	[[Category: Deshmukh, M.]]		[[Category: Deshmukh, M.]]
	[[Category: Gross, J.]]		[[Category: Gross, J.]]
Line 41:		Line 40:
	[[Category: Rna-binding]]		[[Category: Rna-binding]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 08~~:39:~~32 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 01:37:44 2009''

OCA at 05:39, 29 July 2008

2008-07-29T05:39:35Z

← Older revision		Revision as of 05:39, 29 July 2008
Line 1:		Line 1:
	[[Image:2jvb.~~jpg~~\|left\|200px]]		{{Seed}}
			[[Image:2jvb.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_2jvb\| PDB=2jvb \| SCENE= }}		{{STRUCTURE_2jvb\| PDB=2jvb \| SCENE= }}

	~~'''~~Solution Structure of Catalytic Domain of yDcp2~~'''~~		===Solution Structure of Catalytic Domain of yDcp2===


	~~==Overview==~~		<!--
	~~Cap hydrolysis by Dcp2 is a critical step in several eukaryotic mRNA decay pathways. Processing requires access to cap-proximal nucleotides and the coordinated assembly of a decapping mRNP~~, ~~but the mechanism of substrate recognition and regulation by protein interactions have remained elusive. Using NMR spectroscopy and kinetic analyses~~, ~~we show that yeast Dcp2 resolves interactions with~~ the ~~cap and RNA body using a bipartite surface that forms a channel intersecting~~ the ~~catalytic and regulatory Dcp1-binding domains~~. ~~The interaction with cap~~ is ~~weak but specific and requires binding of~~ the ~~RNA body to a dynamic interface~~. ~~The catalytic step is stimulated by Dcp1 and its interaction domain, likely through a substrate~~-~~induced conformational change. Thus, activation of the decapping mRNP is restricted by access to 5'~~-~~proximal nucleotides, a feature that could act as a checkpoint in mRNA metabolism.~~		The line below this paragraph, {{ABSTRACT_PUBMED_18280238}}, adds the Publication Abstract to the page
			(as it appears on PubMed at http://www.pubmed.gov), where 18280238 is the PubMed ID number.
			-->
			{{ABSTRACT_PUBMED_18280238}}

	==About this Structure==		==About this Structure==
	2JVB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JVB OCA].		2JVB is a [[Single protein]] structure of 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=2JVB OCA].

	==Reference==		==Reference==
Line 36:		Line 40:
	[[Category: Phosphorylation]]		[[Category: Phosphorylation]]
	[[Category: Rna-binding]]		[[Category: Rna-binding]]
	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun May 4 09~~:19:41 2008''
			''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 08:39:32 2008''