5kes - Revision history

OCA at 10:12, 14 June 2023

OCA — Wed, 14 Jun 2023 10:12:47 GMT

←Older revision		Revision as of 10:12, 14 June 2023
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	==Solution structure of the yeast Ddi1 HDD domain==		==Solution structure of the yeast Ddi1 HDD domain==
-	<StructureSection load='5kes' size='340' side='right'caption='[[5kes~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='5kes' size='340' side='right'caption='[[5kes]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kes]] 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=5KES OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KES FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kes]] 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=5KES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KES FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDI1, VSM1, YER143W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5kes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kes OCA], [https://pdbe.org/5kes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kes RCSB], [https://www.ebi.ac.uk/pdbsum/5kes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kes 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=5kes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kes OCA], [~~http~~://pdbe.org/5kes PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kes RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kes PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kes ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DDI1_YEAST DDI1_YEAST]] Acts as a linker between the 19S proteasome and polyubiquitinated proteins like the HO endonuclease and UFO1 via UBA domain interactions with ubiquitin for their subsequent degradation. Required for S-phase checkpoint control. Appears to act as negative regulator of constitutive exocytosis. May act at the level of secretory vesicle docking and fusion as a competitive inhibitor of SNARE assembly.<ref>PMID:10330187</ref> <ref>PMID:11238935</ref> <ref>PMID:12051757</ref> <ref>PMID:12925750</ref> <ref>PMID:15964793</ref> <ref>PMID:17144915</ref> <ref>PMID:16478980</ref>	+	[https://www.uniprot.org/uniprot/DDI1_YEAST DDI1_YEAST] Acts as a linker between the 19S proteasome and polyubiquitinated proteins like the HO endonuclease and UFO1 via UBA domain interactions with ubiquitin for their subsequent degradation. Required for S-phase checkpoint control. Appears to act as negative regulator of constitutive exocytosis. May act at the level of secretory vesicle docking and fusion as a competitive inhibitor of SNARE assembly.<ref>PMID:10330187</ref> <ref>PMID:11238935</ref> <ref>PMID:12051757</ref> <ref>PMID:12925750</ref> <ref>PMID:15964793</ref> <ref>PMID:17144915</ref> <ref>PMID:16478980</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gehring, K]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Ratcliffe, C]]	+	[[Category: Gehring K]]
-	[[Category: Saskova, K]]	+	[[Category: Ratcliffe C]]
-	[[Category: Trempe, J F]]	+	[[Category: Saskova K]]
-	[[Category: Veverka, V]]	+	[[Category: Trempe J-F]]
-	~~[[Category: Dna repair]]~~	+	[[Category: Veverka V]]
-	~~[[Category: Helical bundle]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:09, 8 January 2020

OCA — Wed, 08 Jan 2020 08:09:12 GMT

←Older revision		Revision as of 08:09, 8 January 2020
Line 1:		Line 1:

	==Solution structure of the yeast Ddi1 HDD domain==		==Solution structure of the yeast Ddi1 HDD domain==
-	<StructureSection load='5kes' size='340' side='right' caption='[[5kes]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='5kes' size='340' side='right'caption='[[5kes]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kes]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KES FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kes]] 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=5KES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KES 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=5kes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kes OCA], [http://pdbe.org/5kes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kes RCSB], [http://www.ebi.ac.uk/pdbsum/5kes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kes ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DDI1, VSM1, YER143W ([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=5kes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kes OCA], [http://pdbe.org/5kes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kes RCSB], [http://www.ebi.ac.uk/pdbsum/5kes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kes ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Gehring, K]]		[[Category: Gehring, K]]
	[[Category: Ratcliffe, C]]		[[Category: Ratcliffe, C]]

OCA at 21:33, 5 October 2016

OCA — Wed, 05 Oct 2016 21:33:10 GMT

←Older revision		Revision as of 21:33, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kes is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Solution structure of the yeast Ddi1 HDD domain==
		+	<StructureSection load='5kes' size='340' side='right' caption='[[5kes]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kes]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KES OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KES 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=5kes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kes OCA], [http://pdbe.org/5kes PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kes RCSB], [http://www.ebi.ac.uk/pdbsum/5kes PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kes ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DDI1_YEAST DDI1_YEAST]] Acts as a linker between the 19S proteasome and polyubiquitinated proteins like the HO endonuclease and UFO1 via UBA domain interactions with ubiquitin for their subsequent degradation. Required for S-phase checkpoint control. Appears to act as negative regulator of constitutive exocytosis. May act at the level of secretory vesicle docking and fusion as a competitive inhibitor of SNARE assembly.<ref>PMID:10330187</ref> <ref>PMID:11238935</ref> <ref>PMID:12051757</ref> <ref>PMID:12925750</ref> <ref>PMID:15964793</ref> <ref>PMID:17144915</ref> <ref>PMID:16478980</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The eukaryotic Ddi1 family is defined by a conserved retroviral aspartyl protease-like (RVP) domain found in association with a ubiquitin-like (UBL) domain. Ddi1 from Saccharomyces cerevisiae additionally contains a ubiquitin-associated (UBA) domain. The substrate specificity and role of the protease domain in the biological functions of the Ddi family remain unclear. Yeast Ddi1 has been implicated in the regulation of cell cycle progression, DNA-damage repair, and exocytosis. Here, we investigated the multi-domain structure of yeast Ddi1 using X-ray crystallography, nuclear magnetic resonance, and small-angle X-ray scattering. The crystal structure of the RVP domain sheds light on a putative substrate recognition site involving a conserved loop. Isothermal titration calorimetry confirms that both UBL and UBA domains bind ubiquitin, and that Ddi1 binds K48-linked diubiquitin with enhanced affinity. The solution NMR structure of a helical domain that precedes the protease displays tertiary structure similarity to DNA-binding domains from transcription regulators. Our structural studies suggest that the helical domain could serve as a landing platform for substrates in conjunction with attached ubiquitin chains binding to the UBL and UBA domains.

-	~~Authors: Trempe, J.~~-F., ~~Ratcliffe~~, C., ~~Veverka~~, V., ~~Saskova~~, K., ~~Gehring~~, K.	+	Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.,Trempe JF, Saskova KG, Siva M, Ratcliffe CD, Veverka V, Hoegl A, Menade M, Feng X, Shenker S, Svoboda M, Kozisek M, Konvalinka J, Gehring K Sci Rep. 2016 Sep 20;6:33671. doi: 10.1038/srep33671. PMID:27646017<ref>PMID:27646017</ref>

-	~~Description: Solution structure~~ of the ~~yeast Ddi1 HDD domain~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Veverka, V]]~~	+	<div class="pdbe-citations 5kes" style="background-color:#fffaf0;"></div>
-	~~[[Category: Saskova, K]]~~	+	== References ==
-	~~[[Category: Ratcliffe, C]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gehring, K]]		[[Category: Gehring, K]]
-	[[Category: Trempe, J.-F]]	+	[[Category: Ratcliffe, C]]
		+	[[Category: Saskova, K]]
		+	[[Category: Trempe, J F]]
		+	[[Category: Veverka, V]]
		+	[[Category: Dna repair]]
		+	[[Category: Helical bundle]]
		+	[[Category: Unknown function]]

OCA at 00:18, 13 July 2016

OCA — Wed, 13 Jul 2016 00:18:54 GMT

←Older revision		Revision as of 00:18, 13 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5kes is ON HOLD	+	The entry 5kes is ON HOLD until Paper Publication

	Authors: Trempe, J.-F., Ratcliffe, C., Veverka, V., Saskova, K., Gehring, K.		Authors: Trempe, J.-F., Ratcliffe, C., Veverka, V., Saskova, K., Gehring, K.

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

OCA — Thu, 23 Jun 2016 21:31:15 GMT

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

←Older revision

Revision as of 21:31, 23 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kes is ON HOLD Authors: Trempe, J.-F., Ratcliffe, C., Veverka, V., Saskova, K., Gehring, K. Description: Solution structure of the yeast Ddi1 HDD ...

OCA — Thu, 23 Jun 2016 21:31:13 GMT

New page: '''Unreleased structure''' The entry 5kes is ON HOLD Authors: Trempe, J.-F., Ratcliffe, C., Veverka, V., Saskova, K., Gehring, K. Description: Solution structure of the yeast Ddi1 HDD ...

New page

'''Unreleased structure'''

The entry 5kes is ON HOLD

Authors: Trempe, J.-F., Ratcliffe, C., Veverka, V., Saskova, K., Gehring, K.

Description: Solution structure of the yeast Ddi1 HDD domain
[[Category: Unreleased Structures]]
[[Category: Veverka, V]]
[[Category: Saskova, K]]
[[Category: Ratcliffe, C]]
[[Category: Gehring, K]]
[[Category: Trempe, J.-F]]