7o2l - Revision history

OCA at 12:43, 1 February 2024

2024-02-01T12:43:41Z

←Older revision		Revision as of 12:43, 1 February 2024
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	==Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)==		==Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)==
-	<StructureSection load='7o2l' size='340' side='right'caption='[[7o2l]]' scene=''>	+	<StructureSection load='7o2l' size='340' side='right'caption='[[7o2l]], [[Resolution\|resolution]] 3.00Å' 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=7O2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O2L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7o2l]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O2L 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=7o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o2l OCA], [https://pdbe.org/7o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o2l RCSB], [https://www.ebi.ac.uk/pdbsum/7o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o2l 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]] 3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=V08:(2+{R},3+{S})-3-methanoyl-4-methyl-2-hydroxy-pentanoic+acid'>V08</scene></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=7o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o2l OCA], [https://pdbe.org/7o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o2l RCSB], [https://www.ebi.ac.uk/pdbsum/7o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o2l ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PSB2_YEAST PSB2_YEAST] The proteasome degrades poly-ubiquitinated proteins in the cytoplasm and in the nucleus. It is essential for the regulated turnover of proteins and for the removal of misfolded proteins. The proteasome is a multicatalytic proteinase complex that is characterized by its ability to cleave peptides with Arg, Phe, Tyr, Leu, and Glu adjacent to the leaving group at neutral or slightly basic pH. It has an ATP-dependent proteolytic activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microorganisms contribute to the biology and physiology of eukaryotic hosts and affect other organisms through natural products. Xenorhabdus and Photorhabdus (XP) living in mutualistic symbiosis with entomopathogenic nematodes generate natural products to mediate bacteria-nematode-insect interactions. However, a lack of systematic analysis of the XP biosynthetic gene clusters (BGCs) has limited the understanding of how natural products affect interactions between the organisms. Here we combine pangenome and sequence similarity networks to analyse BGCs from 45 XP strains that cover all sequenced strains in our collection and represent almost all XP taxonomy. The identified 1,000 BGCs belong to 176 families. The most conserved families are denoted by 11 BGC classes. We homologously (over)express the ubiquitous and unique BGCs and identify compounds featuring unusual architectures. The bioactivity evaluation demonstrates that the prevalent compounds are eukaryotic proteasome inhibitors, virulence factors against insects, metallophores and insect immunosuppressants. These findings explain the functional basis of bacterial natural products in this tripartite relationship.
		+
		+	Global analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.,Shi YM, Hirschmann M, Shi YN, Ahmed S, Abebew D, Tobias NJ, Grun P, Crames JJ, Poschel L, Kuttenlochner W, Richter C, Herrmann J, Muller R, Thanwisai A, Pidot SJ, Stinear TP, Groll M, Kim Y, Bode HB Nat Chem. 2022 Jun;14(6):701-712. doi: 10.1038/s41557-022-00923-2. Epub 2022 Apr , 25. PMID:35469007<ref>PMID:35469007</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7o2l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proteasome 3D structures\|Proteasome 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae]]
	[[Category: Abebew D]]		[[Category: Abebew D]]
	[[Category: Bode H]]		[[Category: Bode H]]

OCA at 14:46, 31 August 2022

2022-08-31T14:46:00Z

←Older revision		Revision as of 14:46, 31 August 2022
Line 1:		Line 1:

-	====	+	==Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)==
	<StructureSection load='7o2l' size='340' side='right'caption='[[7o2l]]' scene=''>		<StructureSection load='7o2l' size='340' side='right'caption='[[7o2l]]' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7O2L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7O2L 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=7o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o2l OCA], [https://pdbe.org/7o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o2l RCSB], [https://www.ebi.ac.uk/pdbsum/7o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o2l ProSAT]</span></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=7o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o2l OCA], [https://pdbe.org/7o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o2l RCSB], [https://www.ebi.ac.uk/pdbsum/7o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o2l ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Abebew D]]
		+	[[Category: Bode H]]
		+	[[Category: Crames JJ]]
		+	[[Category: Groll M]]
		+	[[Category: Gruen P]]
		+	[[Category: Herrmann J]]
		+	[[Category: Hirschmann M]]
		+	[[Category: Kim Y]]
		+	[[Category: Kuttenlochner W]]
		+	[[Category: Mueller R]]
		+	[[Category: Pidot SJ]]
		+	[[Category: Poeschel L]]
		+	[[Category: Richter C]]
		+	[[Category: Shabbir A]]
		+	[[Category: Shi YM]]
		+	[[Category: Shi YN]]
		+	[[Category: Stinear TP]]
		+	[[Category: Thanwisai A]]
		+	[[Category: Tobias NJ]]

OCA at 09:45, 13 April 2022

2022-04-13T09:45:55Z

←Older revision		Revision as of 09:45, 13 April 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7o2l ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7o2l' size='340' side='right'caption='[[7o2l]]' scene=''>
-	~~Authors~~: ~~Shi, Y~~.M.~~, Hirschmann, M~~.~~, Shi, Y~~.N., Shabbir, A., Abebew, D., Tobias, N.J., Gruen, P., Crames, J.J., Poeschel, L., Kuttenlochner, W., Richter, C., Herrmann, J., Mueller, R., Thanwisai, A., Pidot, S.J., Stinear, T.P., Groll, M., Kim, Y., Bode, H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Yeast 20S proteasome in complex with~~ the ~~covalently bound inhibitor~~ b~~-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)~~	+	</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=7o2l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7o2l OCA], [https://pdbe.org/7o2l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7o2l RCSB], [https://www.ebi.ac.uk/pdbsum/7o2l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7o2l ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	~~[[Category: Tobias, N~~.~~J]]~~	+	__TOC__
-	~~[[Category~~: ~~Kuttenlochner, W]]~~	+	</StructureSection>
-	[~~[Category~~: ~~Shi, Y~~.M]]	+	[[Category: Large Structures]]
-	~~[[Category: Mueller~~, ~~R]]~~	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Poeschel, L]]~~	+
-	~~[[Category: Crames, J~~.J]]	+
-	~~[[Category: Bode~~, ~~H]]~~	+
-	[~~[Category~~: ~~Stinear, T~~.P]]	+
-	~~[[Category: Abebew~~, ~~D]]~~	+
-	[~~[Category~~: ~~Shabbir, A]]~~	+
-	~~[[Category: Shi, Y~~.N]]	+
-	~~[[Category: Hirschmann~~, ~~M]]~~	+
-	[~~[Category~~: ~~Kim, Y~~]]	+
-	~~[[Category: Groll~~, ~~M]]~~	+
-	[~~[Category~~: ~~Pidot, S~~.J]]	+
-	~~[[Category: Richter, C]]~~	+
-	~~[[Category: Thanwisai, A]]~~	+
-	[[Category: ~~Herrmann, J~~]]	+
-	[[Category: ~~Gruen, P~~]]	+

OCA: Protected "7o2l" [edit=sysop:move=sysop]

2021-04-07T04:55:22Z

Protected "7o2l" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:55, 7 April 2021

OCA: New page: '''Unreleased structure''' The entry 7o2l is ON HOLD until Paper Publication Authors: Shi, Y.M., Hirschmann, M., Shi, Y.N., Shabbir, A., Abebew, D., Tobias, N.J., Gruen, P., Crames, J.J...

2021-04-07T04:55:20Z

New page: '''Unreleased structure''' The entry 7o2l is ON HOLD until Paper Publication Authors: Shi, Y.M., Hirschmann, M., Shi, Y.N., Shabbir, A., Abebew, D., Tobias, N.J., Gruen, P., Crames, J.J...

New page

'''Unreleased structure'''

The entry 7o2l is ON HOLD until Paper Publication

Authors: Shi, Y.M., Hirschmann, M., Shi, Y.N., Shabbir, A., Abebew, D., Tobias, N.J., Gruen, P., Crames, J.J., Poeschel, L., Kuttenlochner, W., Richter, C., Herrmann, J., Mueller, R., Thanwisai, A., Pidot, S.J., Stinear, T.P., Groll, M., Kim, Y., Bode, H.

Description: Yeast 20S proteasome in complex with the covalently bound inhibitor b-lactone (2R,3S)-3-isopropyl-4-oxo-2-oxetane-carboxylate (IOC)
[[Category: Unreleased Structures]]
[[Category: Tobias, N.J]]
[[Category: Kuttenlochner, W]]
[[Category: Shi, Y.M]]
[[Category: Mueller, R]]
[[Category: Poeschel, L]]
[[Category: Crames, J.J]]
[[Category: Bode, H]]
[[Category: Stinear, T.P]]
[[Category: Abebew, D]]
[[Category: Shabbir, A]]
[[Category: Shi, Y.N]]
[[Category: Hirschmann, M]]
[[Category: Kim, Y]]
[[Category: Groll, M]]
[[Category: Pidot, S.J]]
[[Category: Richter, C]]
[[Category: Thanwisai, A]]
[[Category: Herrmann, J]]
[[Category: Gruen, P]]