6npw - Revision history

OCA at 06:57, 11 October 2023

2023-10-11T06:57:41Z

←Older revision		Revision as of 06:57, 11 October 2023
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	<StructureSection load='6npw' size='340' side='right'caption='[[6npw]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='6npw' size='340' side='right'caption='[[6npw]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6npw]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Drome Drome~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPW OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6npw]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_RM11-1a Saccharomyces cerevisiae RM11-1a]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NPW FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PO4:PHOSPHATE+ION'>PO4</scene~~></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.486Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SEP~~:~~PHOSPHOSERINE~~'>~~SEP~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">Sym, CG2097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), Ssu72, CG14216, Dmel_CG14216 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=6npw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npw OCA], [https://pdbe.org/6npw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6npw RCSB], [https://www.ebi.ac.uk/pdbsum/6npw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6npw 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=6npw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npw OCA], [~~http~~://pdbe.org/6npw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6npw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6npw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6npw ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/SYMPK_DROME SYMPK_DROME]] Component of a protein complex required for cotranscriptional processing of 3'-ends of polyadenylated and histone pre-mRNA.<ref>PMID:18042462</ref> <ref>PMID:19450530</ref>	+	[https://www.uniprot.org/uniprot/SYMPK_DROME SYMPK_DROME] Component of a protein complex required for cotranscriptional processing of 3'-ends of polyadenylated and histone pre-mRNA.<ref>PMID:18042462</ref> <ref>PMID:19450530</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6npw" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6npw" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Symplekin\|Symplekin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Drome~~]]	+	[[Category: Drosophila melanogaster]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Irani, S~~]]	+	[[Category: Saccharomyces cerevisiae RM11-1a]]
-	[[Category: ~~Zhang, Y~~]]	+	[[Category: Irani S]]
-	[[Category: ~~Ctd of rna pol ii]]~~	+	[[Category: Zhang Y]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Phosphatase~~]]	+

OCA at 23:09, 5 June 2019

2019-06-05T23:09:14Z

←Older revision		Revision as of 23:09, 5 June 2019
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	<StructureSection load='6npw' size='340' side='right'caption='[[6npw]], [[Resolution\|resolution]] 2.49Å' scene=''>		<StructureSection load='6npw' size='340' side='right'caption='[[6npw]], [[Resolution\|resolution]] 2.49Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6npw]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPW FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6npw]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Drome Drome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPW FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Sym, CG2097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME]), Ssu72, CG14216, Dmel_CG14216 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7227 DROME])</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=6npw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npw OCA], [http://pdbe.org/6npw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npw RCSB], [http://www.ebi.ac.uk/pdbsum/6npw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npw 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=6npw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npw OCA], [http://pdbe.org/6npw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npw RCSB], [http://www.ebi.ac.uk/pdbsum/6npw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npw ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Drome]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Irani, S]]		[[Category: Irani, S]]

OCA at 07:02, 24 April 2019

2019-04-24T07:02:10Z

←Older revision		Revision as of 07:02, 24 April 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6npw is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==SSu72/Sympk in complex with Ser2/Ser5 phosphorylated peptide==
		+	<StructureSection load='6npw' size='340' side='right'caption='[[6npw]], [[Resolution\|resolution]] 2.49Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6npw]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NPW OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NPW FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SEP:PHOSPHOSERINE'>SEP</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6npw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6npw OCA], [http://pdbe.org/6npw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6npw RCSB], [http://www.ebi.ac.uk/pdbsum/6npw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6npw ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SYMPK_DROME SYMPK_DROME]] Component of a protein complex required for cotranscriptional processing of 3'-ends of polyadenylated and histone pre-mRNA.<ref>PMID:18042462</ref> <ref>PMID:19450530</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The C-terminal domain of RNA polymerase II (CTD) contains a repetitive heptad sequence (YSPTSPS) whose phosphorylation states coordinate eukaryotic transcription by recruiting protein regulators. The precise placement and removal of phosphate groups on specific residues of the CTD are critical for the fidelity and effectiveness of RNA polymerase II-mediated transcription. During transcriptional elongation, phosphoryl-Ser5 (pSer5) is gradually dephosphorylated by CTD phosphatases, while Ser2 phosphorylation is accumulating. Using MS, X-ray crystallography, protein engineering, and immunoblotting analyses, here we investigated the structure and function of SSU72 homolog, RNA polymerase II CTD phosphatase (Ssu72, from Drosophila melanogaster), an essential CTD phosphatase that dephosphorylates pSer5 at the transition from elongation to termination, to determine the mechanism by which Ssu72 distinguishes the highly similar pSer2 and pSer5 CTDs. We found that Ssu72 dephosphorylates pSer5 effectively, but only has low activities toward pSer7 and pSer2. The structural analysis revealed that Ssu72 requires that the proline residue in the substrate's SP motif is in the cis configuration, forming a tight beta-turn for recognition by Ssu72. We also noted that residues flanking the SP motif, such as the bulky Tyr1 next to Ser2, prevent the formation of such configuration and enable Ssu72 to distinguish among the different SP motifs. The phosphorylation of Tyr-1 further prohibited Ssu72 binding to pSer2 and thereby prevented untimely Ser2 dephosphorylation. Our results reveal critical roles for Tyr1 in differentiating the phosphorylation states of Ser2/Ser5 of CTD in RNA polymerase II, which occur at different stages of transcription.

-	~~Authors~~:	+	Structural determinants for accurate dephosphorylation of RNA polymerase II by its cognate CTD phosphatase during eukaryotic transcription.,Irani S, Sipe SN, Yang W, Burkholder NT, Lin B, Sim K, Matthews WL, Brodbelt JS, Zhang Y J Biol Chem. 2019 Apr 10. pii: RA119.007697. doi: 10.1074/jbc.RA119.007697. PMID:30971428<ref>PMID:30971428</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6npw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Irani, S]]
		+	[[Category: Zhang, Y]]
		+	[[Category: Ctd of rna pol ii]]
		+	[[Category: Hydrolase]]
		+	[[Category: Phosphatase]]

OCA at 07:37, 13 February 2019

2019-02-13T07:37:03Z

←Older revision		Revision as of 07:37, 13 February 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2019-01-30T06:44:28Z

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

←Older revision

Revision as of 06:44, 30 January 2019

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

2019-01-30T06:44:27Z

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

New page

'''Unreleased structure'''

The entry 6npw is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]