5jp4 - Revision history

OCA at 07:47, 7 February 2024

2024-02-07T07:47:57Z

←Older revision		Revision as of 07:47, 7 February 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JP4 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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [https://pdbe.org/5jp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [https://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></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]] 2.043Å</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [https://pdbe.org/5jp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [https://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO] 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:15671491</ref>		[https://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO] 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:15671491</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The removal of the 5' 7-methylguanosine mRNA cap structure (decapping) is a central step in the 5'-3' mRNA degradation pathway and is performed by the Dcp1:Dcp2 decapping complex. The activity of this complex is tightly regulated to prevent premature degradation of the transcript. Here, we establish that the aromatic groove of the EVH1 domain of Schizosaccharomyces pombe Dcp1 can interact with proline-rich sequences in the exonuclease Xrn1, the scaffolding protein Pat1, the helicase Dhh1, and the C-terminal disordered region of Dcp2. We show that this region of Dcp1 can also recruit a previously unidentified enhancer of decapping protein (Edc1) and solved the crystal structure of the complex. NMR relaxation dispersion experiments reveal that the Dcp1 binding site can adopt multiple conformations, thus providing the plasticity that is required to accommodate different ligands. We show that the activator Edc1 makes additional contacts with the regulatory domain of Dcp2 and that an activation motif in Edc1 increases the RNA affinity of Dcp1:Dcp2. Our data support a model where Edc1 stabilizes the RNA in the active site, which results in enhanced decapping rates. In summary, we show that multiple decapping factors, including the Dcp2 C-terminal region, compete with Edc1 for Dcp1 binding. Our data thus reveal a network of interactions that can fine-tune the catalytic activity of the decapping complex.
-
-	The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface.,Wurm JP, Overbeck J, Sprangers R RNA. 2016 Sep;22(9):1360-72. doi: 10.1261/rna.057315.116. Epub 2016 Jun 28. PMID:27354705<ref>PMID:27354705</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5jp4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:30, 22 March 2023

2023-03-22T07:30:59Z

←Older revision		Revision as of 07:30, 22 March 2023
Line 3:		Line 3:
	<StructureSection load='5jp4' size='340' side='right'caption='[[5jp4]], [[Resolution\|resolution]] 2.04Å' scene=''>		<StructureSection load='5jp4' size='340' side='right'caption='[[5jp4]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cbs_356 Cbs 356~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dcp1, SPBC3B9.21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), SPAC18G6.09c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</td></tr>	+	</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [https://pdbe.org/5jp4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [https://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [~~http~~://pdbe.org/5jp4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO]] 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:15671491</ref>	+	[https://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO] 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:15671491</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The removal of the 5' 7-methylguanosine mRNA cap structure (decapping) is a central step in the 5'-3' mRNA degradation pathway and is performed by the Dcp1:Dcp2 decapping complex. The activity of this complex is tightly regulated to prevent premature degradation of the transcript. Here, we establish that the aromatic groove of the EVH1 domain of Schizosaccharomyces pombe Dcp1 can interact with proline-rich sequences in the exonuclease Xrn1, the scaffolding protein Pat1, the helicase Dhh1, and the C-terminal disordered region of Dcp2. We show that this region of Dcp1 can also recruit a previously unidentified enhancer of decapping protein (Edc1) and solved the crystal structure of the complex. NMR relaxation dispersion experiments reveal that the Dcp1 binding site can adopt multiple conformations, thus providing the plasticity that is required to accommodate different ligands. We show that the activator Edc1 makes additional contacts with the regulatory domain of Dcp2 and that an activation motif in Edc1 increases the RNA affinity of Dcp1:Dcp2. Our data support a model where Edc1 stabilizes the RNA in the active site, which results in enhanced decapping rates. In summary, we show that multiple decapping factors, including the Dcp2 C-terminal region, compete with Edc1 for Dcp1 binding. Our data thus reveal a network of interactions that can fine-tune the catalytic activity of the decapping complex.
		+
		+	The S. pombe mRNA decapping complex recruits cofactors and an Edc1-like activator through a single dynamic surface.,Wurm JP, Overbeck J, Sprangers R RNA. 2016 Sep;22(9):1360-72. doi: 10.1261/rna.057315.116. Epub 2016 Jun 28. PMID:27354705<ref>PMID:27354705</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5jp4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Cbs 356]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Sprangers, R~~]]	+	[[Category: Schizosaccharomyces pombe]]
-	[[Category: ~~Wurm, J P~~]]	+	[[Category: Sprangers R]]
-	[[Category: ~~Complex]]~~	+	[[Category: Wurm JP]]
-	~~[[Category: Decapping]]~~	+
-	~~[[Category: Evh1]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Mrna]]~~	+
-	~~[[Category: Peptide binding protein~~]]	+

OCA at 11:32, 17 June 2020

2020-06-17T11:32:44Z

←Older revision		Revision as of 11:32, 17 June 2020
Line 1:		Line 1:

	==Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC==		==Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC==
-	<StructureSection load='5jp4' size='340' side='right' caption='[[5jp4]], [[Resolution\|resolution]] 2.04Å' scene=''>	+	<StructureSection load='5jp4' size='340' side='right'caption='[[5jp4]], [[Resolution\|resolution]] 2.04Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cbs_356 Cbs 356]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>
-	</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [http://pdbe.org/5jp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">dcp1, SPBC3B9.21 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356]), SPAC18G6.09c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4896 CBS 356])</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [http://pdbe.org/5jp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 13:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cbs 356]]
		+	[[Category: Large Structures]]
	[[Category: Sprangers, R]]		[[Category: Sprangers, R]]
	[[Category: Wurm, J P]]		[[Category: Wurm, J P]]

OCA at 11:09, 15 December 2016

2016-12-15T11:09:46Z

←Older revision		Revision as of 11:09, 15 December 2016
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>
-	</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [http://pdbe.org/5jp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp4 PDBsum]</span></td></tr>	+	</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [http://pdbe.org/5jp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jp4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 12:		Line 12:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Sprangers , R]]	+	[[Category: Sprangers, R]]
	[[Category: Wurm, J P]]		[[Category: Wurm, J P]]
	[[Category: Complex]]		[[Category: Complex]]

OCA at 06:11, 2 June 2016

2016-06-02T06:11:31Z

←Older revision		Revision as of 06:11, 2 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jp4 is ~~ON HOLD~~	+	==Crystal structure of S. pombe Dcp1 in complex with the decapping enhancer EDC==
-		+	<StructureSection load='5jp4' size='340' side='right' caption='[[5jp4]], [[Resolution\|resolution]] 2.04Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5jp4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JP4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JP4 FirstGlance]. <br>
-	~~Description~~:	+	</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=5jp4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jp4 OCA], [http://pdbe.org/5jp4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jp4 RCSB], [http://www.ebi.ac.uk/pdbsum/5jp4 PDBsum]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DCP1_SCHPO DCP1_SCHPO]] 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:15671491</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Sprangers , R]]
		+	[[Category: Wurm, J P]]
		+	[[Category: Complex]]
		+	[[Category: Decapping]]
		+	[[Category: Evh1]]
		+	[[Category: Hydrolase]]
		+	[[Category: Mrna]]
		+	[[Category: Peptide binding protein]]

OCA: Protected "5jp4" [edit=sysop:move=sysop]

2016-05-15T15:41:41Z

Protected "5jp4" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:41, 15 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jp4 is ON HOLD Authors: Description: Category: Unreleased Structures

2016-05-15T15:41:40Z

New page: '''Unreleased structure''' The entry 5jp4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5jp4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]