6y6r - Revision history

OCA at 13:20, 24 January 2024

OCA — Wed, 24 Jan 2024 13:20:36 GMT

←Older revision		Revision as of 13:20, 24 January 2024
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	<StructureSection load='6y6r' size='340' side='right'caption='[[6y6r]], [[Resolution\|resolution]] 3.32Å' scene=''>		<StructureSection load='6y6r' size='340' side='right'caption='[[6y6r]], [[Resolution\|resolution]] 3.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y6r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y6r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6R FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>MINDY1, FAM63A, KIAA1390 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN])</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]] 3.32Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1~~]~~, with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~3.~~4.19.12 3.4.19.12] </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=6y6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6r OCA], [https://pdbe.org/6y6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6r RCSB], [https://www.ebi.ac.uk/pdbsum/6y6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6r 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=6y6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6r OCA], [https://pdbe.org/6y6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6r RCSB], [https://www.ebi.ac.uk/pdbsum/6y6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6r ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/MINY1_HUMAN MINY1_HUMAN]] Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.<ref>PMID:27292798</ref> <ref>PMID:28082312</ref>	+	[https://www.uniprot.org/uniprot/MINY1_HUMAN MINY1_HUMAN] Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.<ref>PMID:27292798</ref> <ref>PMID:28082312</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ubiquitinyl hydrolase 1~~]]	+	[[Category: Abdul Rehman SA]]
-	[[Category: Kulathu, Y]]	+	[[Category: Kulathu Y]]
-	~~[[Category: Rehman, S A.Abdul]]~~	+
-	~~[[Category: Cysteine protease]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Isopeptidase and ubiquitin binding~~]]	+

OCA at 12:45, 13 October 2021

OCA — Wed, 13 Oct 2021 12:45:58 GMT

←Older revision		Revision as of 12:45, 13 October 2021
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	==Crystal structure of MINDY1 T335D mutant==		==Crystal structure of MINDY1 T335D mutant==
-	<StructureSection load='6y6r' size='340' side='right'caption='[[6y6r]]' scene=''>	+	<StructureSection load='6y6r' size='340' side='right'caption='[[6y6r]], [[Resolution\|resolution]] 3.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6R FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y6r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6R 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=6y6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6r OCA], [https://pdbe.org/6y6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6r RCSB], [https://www.ebi.ac.uk/pdbsum/6y6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6r ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MINDY1, FAM63A, KIAA1390 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ubiquitinyl_hydrolase_1 Ubiquitinyl hydrolase 1], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.19.12 3.4.19.12] </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=6y6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6r OCA], [https://pdbe.org/6y6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6r RCSB], [https://www.ebi.ac.uk/pdbsum/6y6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6r ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/MINY1_HUMAN MINY1_HUMAN]] Hydrolase that can specifically remove 'Lys-48'-linked conjugated ubiquitin from proteins. Has exodeubiquitinase activity and has a preference for long polyubiquitin chains. May play a regulatory role at the level of protein turnover.<ref>PMID:27292798</ref> <ref>PMID:28082312</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Of the eight distinct polyubiquitin (polyUb) linkages that can be assembled, the roles of K48-linked polyUb (K48-polyUb) are the most established, with K48-polyUb modified proteins being targeted for degradation. MINDY1 and MINDY2 are members of the MINDY family of deubiquitinases (DUBs) that have exquisite specificity for cleaving K48-polyUb, yet we have a poor understanding of their catalytic mechanism. Here, we analyze the crystal structures of MINDY1 and MINDY2 alone and in complex with monoUb, di-, and penta-K48-polyUb, identifying 5 distinct Ub binding sites in the catalytic domain that explain how these DUBs sense both Ub chain length and linkage type to cleave K48-polyUb chains. The activity of MINDY1/2 is inhibited by the Cys-loop, and we find that substrate interaction relieves autoinhibition to activate these DUBs. We also find that MINDY1/2 use a non-canonical catalytic triad composed of Cys-His-Thr. Our findings highlight multiple layers of regulation modulating DUB activity in MINDY1 and MINDY2.
		+
		+	Mechanism of activation and regulation of deubiquitinase activity in MINDY1 and MINDY2.,Abdul Rehman SA, Armstrong LA, Lange SM, Kristariyanto YA, Grawert TW, Knebel A, Svergun DI, Kulathu Y Mol Cell. 2021 Sep 10. pii: S1097-2765(21)00691-2. doi:, 10.1016/j.molcel.2021.08.024. PMID:34529927<ref>PMID:34529927</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y6r" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Abdul Rehman SA~~]]	+	[[Category: Ubiquitinyl hydrolase 1]]
-	[[Category: Kulathu Y]]	+	[[Category: Kulathu, Y]]
		+	[[Category: Rehman, S A.Abdul]]
		+	[[Category: Cysteine protease]]
		+	[[Category: Hydrolase]]
		+	[[Category: Isopeptidase and ubiquitin binding]]

OCA at 10:29, 31 March 2021

OCA — Wed, 31 Mar 2021 10:29:12 GMT

←Older revision		Revision as of 10:29, 31 March 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6y6r ~~is ON HOLD until Feb 27 2022~~	+	==Crystal structure of MINDY1 T335D mutant==
-		+	<StructureSection load='6y6r' size='340' side='right'caption='[[6y6r]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y6R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y6R FirstGlance]. <br>
-	~~Description~~:	+	</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=6y6r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y6r OCA], [https://pdbe.org/6y6r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y6r RCSB], [https://www.ebi.ac.uk/pdbsum/6y6r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y6r ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Abdul Rehman SA]]
		+	[[Category: Kulathu Y]]

OCA at 08:37, 18 March 2020

OCA — Wed, 18 Mar 2020 08:37:32 GMT

←Older revision		Revision as of 08:37, 18 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y6r is ON HOLD	+	The entry 6y6r is ON HOLD until Feb 27 2022

	Authors:		Authors:

OCA: Protected "6y6r" [edit=sysop:move=sysop]

OCA — Wed, 04 Mar 2020 05:47:35 GMT

Protected "6y6r" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:47, 4 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y6r is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Mar 2020 05:47:34 GMT

New page: '''Unreleased structure''' The entry 6y6r is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6y6r is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]