5knl - Revision history

OCA at 10:04, 27 September 2023

2023-09-27T10:04:21Z

←Older revision		Revision as of 10:04, 27 September 2023
Line 3:		Line 3:
	<StructureSection load='5knl' size='340' side='right'caption='[[5knl]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5knl' size='340' side='right'caption='[[5knl]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5knl]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_34888 Atcc 34888~~] and [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KNL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5knl]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Moesziomyces_antarcticus Moesziomyces antarcticus] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KNL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.5Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ptr3, SPBC1604~~.~~21c, SPBC211.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5&id=284812 Fission yeast]), PAN0_008c3613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84753 ATCC 34888]), ubc15, SPBC1105.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45]~~ </~~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=5knl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knl OCA], [https://pdbe.org/5knl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5knl RCSB], [https://www.ebi.ac.uk/pdbsum/5knl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5knl 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=5knl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knl OCA], [~~http~~://pdbe.org/5knl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5knl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5knl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5knl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/UBA1_SCHPO UBA1_SCHPO]] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP. [[http://www.uniprot.org/uniprot/UBC15_SCHPO UBC15_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref>	+	[https://www.uniprot.org/uniprot/UBA1_SCHPO UBA1_SCHPO] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:

	==See Also==		==See Also==
-	*[[Ubiquitin\|Ubiquitin]]	+	*[[3D structures of Ubiquitin activating enzyme\|3D structures of Ubiquitin activating enzyme]]
-	*[[~~Ubiquitin activating enzyme~~\|~~Ubiquitin activating enzyme~~]]	+	*[[3D structures of ubiquitin\|3D structures of ubiquitin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 34888]]
-	[[Category: E1 ubiquitin-activating enzyme]]
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lv, Z~~]]	+	[[Category: Moesziomyces antarcticus]]
-	[[Category: ~~Olsen, S K]]~~	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	~~[[Category: Williams, K]]~~	+	[[Category: Lv Z]]
-	~~[[Category: Yuan, L]]~~	+	[[Category: Olsen SK]]
-	~~[[Category: Adenylation]]~~	+	[[Category: Williams K]]
-	~~[[Category: Atp~~-~~binding~~]]	+	[[Category: Yuan L]]
-	[[Category: ~~Conformational change~~]]	+
-	[[Category: E1]]	+
-	[[Category: E2]]	+
-	[[Category: ~~Ligase]]~~	+
-	~~[[Category: Thioester]]~~	+
-	~~[[Category: Uba1]]~~	+
-	~~[[Category: Ubc15]]~~	+
-	~~[[Category: Ubiquitin]]~~	+
-	~~[[Category: Ubiquitin e2 binding]]~~	+
-	~~[[Category: Ubiquitination~~]]	+

OCA at 12:19, 25 December 2019

2019-12-25T12:19:49Z

←Older revision		Revision as of 12:19, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin==		==Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin==
-	<StructureSection load='5knl' size='340' side='right' caption='[[5knl]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5knl' size='340' side='right'caption='[[5knl]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5knl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KNL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5knl]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_34888 Atcc 34888] and [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KNL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ptr3, SPBC1604.21c, SPBC211.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), PAN0_008c3613 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=84753 ATCC 34888]), ubc15, SPBC1105.09 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45] </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=5knl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knl OCA], [http://pdbe.org/5knl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5knl RCSB], [http://www.ebi.ac.uk/pdbsum/5knl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5knl 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=5knl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knl OCA], [http://pdbe.org/5knl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5knl RCSB], [http://www.ebi.ac.uk/pdbsum/5knl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5knl ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5knl" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5knl" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ubiquitin\|Ubiquitin]]
		+	*[[Ubiquitin activating enzyme\|Ubiquitin activating enzyme]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 34888]]
	[[Category: E1 ubiquitin-activating enzyme]]		[[Category: E1 ubiquitin-activating enzyme]]
		+	[[Category: Fission yeast]]
		+	[[Category: Large Structures]]
	[[Category: Lv, Z]]		[[Category: Lv, Z]]
	[[Category: Olsen, S K]]		[[Category: Olsen, S K]]

OCA at 07:54, 9 March 2017

2017-03-09T07:54:36Z

←Older revision		Revision as of 07:54, 9 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5knl is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of S. pombe ubiquitin E1 (Uba1) in complex with Ubc15 and ubiquitin==
		+	<StructureSection load='5knl' size='340' side='right' caption='[[5knl]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5knl]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KNL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KNL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/E1_ubiquitin-activating_enzyme E1 ubiquitin-activating enzyme], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.45 6.2.1.45] </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=5knl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5knl OCA], [http://pdbe.org/5knl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5knl RCSB], [http://www.ebi.ac.uk/pdbsum/5knl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5knl ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/UBA1_SCHPO UBA1_SCHPO]] Activates ubiquitin by first adenylating its C-terminal glycine residue with ATP, and thereafter linking this residue to the side chain of a cysteine residue in E1, yielding an ubiquitin-E1 thioester and free AMP. [[http://www.uniprot.org/uniprot/UBC15_SCHPO UBC15_SCHPO]] Catalyzes the covalent attachment of ubiquitin to other proteins. Has a role in the formation of chromatin structures that influence the localization of transcriptional silencing factors.[PROSITE-ProRule:PRU00388]<ref>PMID:12456009</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ubiquitin (Ub) E1 initiates the Ub conjugation cascade by activating and transferring Ub to tens of different E2s. How Ub E1 cooperates with E2s that differ substantially in their predicted E1-interacting residues is unknown. Here, we report the structure of S. pombe Uba1 in complex with Ubc15, a Ub E2 with intrinsically low E1-E2 Ub thioester transfer activity. The structure reveals a distinct Ubc15 binding mode that substantially alters the network of interactions at the E1-E2 interface compared to the only other available Ub E1-E2 structure. Structure-function analysis reveals that the intrinsically low activity of Ubc15 largely results from the presence of an acidic residue at its N-terminal region. Notably, Ub E2 N termini are serine/threonine rich in many other Ub E2s, leading us to hypothesize that phosphorylation of these sites may serve as a novel negative regulatory mechanism of Ub E2 activity, which we demonstrate biochemically and in cell-based assays.

-	~~Authors~~:	+	S. pombe Uba1-Ubc15 Structure Reveals a Novel Regulatory Mechanism of Ubiquitin E2 Activity.,Lv Z, Rickman KA, Yuan L, Williams K, Selvam SP, Woosley AN, Howe PH, Ogretmen B, Smogorzewska A, Olsen SK Mol Cell. 2017 Feb 16;65(4):699-714.e6. doi: 10.1016/j.molcel.2017.01.008. Epub, 2017 Feb 2. PMID:28162934<ref>PMID:28162934</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5knl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: E1 ubiquitin-activating enzyme]]
		+	[[Category: Lv, Z]]
		+	[[Category: Olsen, S K]]
		+	[[Category: Williams, K]]
		+	[[Category: Yuan, L]]
		+	[[Category: Adenylation]]
		+	[[Category: Atp-binding]]
		+	[[Category: Conformational change]]
		+	[[Category: E1]]
		+	[[Category: E2]]
		+	[[Category: Ligase]]
		+	[[Category: Thioester]]
		+	[[Category: Uba1]]
		+	[[Category: Ubc15]]
		+	[[Category: Ubiquitin]]
		+	[[Category: Ubiquitin e2 binding]]
		+	[[Category: Ubiquitination]]

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

2016-07-13T00:37:04Z

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

←Older revision

Revision as of 00:37, 13 July 2016

OCA: New page: '''Unreleased structure''' The entry 5knl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

2016-07-13T00:37:03Z

New page: '''Unreleased structure''' The entry 5knl is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5knl is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]