7oms - Revision history

OCA at 12:53, 1 February 2024

OCA — Thu, 01 Feb 2024 12:53:03 GMT

←Older revision		Revision as of 12:53, 1 February 2024
Line 1:		Line 1:

	==Bs164 in complex with mannocyclophellitol aziridine==		==Bs164 in complex with mannocyclophellitol aziridine==
-	<StructureSection load='7oms' size='340' side='right'caption='[[7oms]]' scene=''>	+	<StructureSection load='7oms' size='340' side='right'caption='[[7oms]], [[Resolution\|resolution]] 2.05Å' 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=7OMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OMS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7oms]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_salyersiae Bacteroides salyersiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OMS 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=7oms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oms OCA], [https://pdbe.org/7oms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oms RCSB], [https://www.ebi.ac.uk/pdbsum/7oms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oms 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]] 2.05Å</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=VKH:(1~{R},2~{R},3~{S},4~{R},5~{R},6~{R})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol'>VKH</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=7oms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oms OCA], [https://pdbe.org/7oms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oms RCSB], [https://www.ebi.ac.uk/pdbsum/7oms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oms ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I9SUA3_9BACE I9SUA3_9BACE]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Exo-beta-mannosidases are a broad class of stereochemically retaining hydrolases that are essential for the breakdown of complex carbohydrate substrates found in all kingdoms of life. Yet the detection of exo-beta-mannosidases in complex biological samples remains challenging, necessitating the development of new methodologies. Cyclophellitol and its analogues selectively label the catalytic nucleophiles of retaining glycoside hydrolases, making them valuable tool compounds. Furthermore, cyclophellitol can be readily redesigned to enable the incorporation of a detection tag, generating activity-based probes (ABPs) that can be used to detect and identify specific glycosidases in complex biological samples. Towards the development of ABPs for exo-beta-mannosidases, we present a concise synthesis of beta-manno-configured cyclophellitol, cyclophellitol aziridine, and N-alkyl cyclophellitol aziridines. We show that these probes covalently label exo-beta-mannosidases from GH families 2, 5, and 164. Structural studies of the resulting complexes support a canonical mechanism-based mode of action in which the active site nucleophile attacks the pseudoanomeric centre to form a stable ester linkage, mimicking the glycosyl enzyme intermediate. Furthermore, we demonstrate activity-based protein profiling using an N-alkyl aziridine derivative by specifically labelling MANBA in mouse kidney tissue. Together, these results show that synthetic manno-configured cyclophellitol analogues hold promise for detecting exo-beta-mannosidases in biological and biomedical research.
		+
		+	Synthesis of broad-specificity activity-based probes for exo-beta-mannosidases.,McGregor NGS, Kuo CL, Beenakker TJM, Wong CS, Offen WA, Armstrong Z, Florea BI, Codee JDC, Overkleeft HS, Aerts JMFG, Davies GJ Org Biomol Chem. 2022 Jan 26;20(4):877-886. doi: 10.1039/d1ob02287c. PMID:35015006<ref>PMID:35015006</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7oms" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides salyersiae]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Aerts JMFG]]		[[Category: Aerts JMFG]]

OCA at 07:01, 2 February 2022

OCA — Wed, 02 Feb 2022 07:01:17 GMT

←Older revision		Revision as of 07:01, 2 February 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7oms ~~is ON HOLD until Paper Publication~~	+	==Bs164 in complex with mannocyclophellitol aziridine==
-		+	<StructureSection load='7oms' size='340' side='right'caption='[[7oms]]' scene=''>
-	~~Authors~~: ~~McGregor, N~~.~~, Beenakker, T~~.~~, Kuo, C~~.L.~~, Wong, C~~.S.~~, Offren, W~~.A.~~, Armstrong, Z~~., ~~Codee, J~~.D.C., ~~Aerts~~, J.M.~~F.G~~., ~~Florea, B~~.I.~~, Overkleeft, H~~., ~~Davies, G~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OMS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OMS FirstGlance]. <br>
-	~~Description: Bs164 in complex with mannocyclophellitol aziridine~~	+	</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=7oms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7oms OCA], [https://pdbe.org/7oms PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7oms RCSB], [https://www.ebi.ac.uk/pdbsum/7oms PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7oms ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Florea, B.I~~]]	+	__TOC__
-	[[Category: ~~Aerts, J.M.F.G~~]]	+	</StructureSection>
-	[[Category: ~~Overkleeft, H~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Mcgregor, N~~]]	+	[[Category: Aerts JMFG]]
-	[[Category: ~~Offren, W.A~~]]	+	[[Category: Armstrong Z]]
-	[[Category: ~~Codee, J.D.C~~]]	+	[[Category: Beenakker T]]
-	[[Category: ~~Davies, G.J~~]]	+	[[Category: Codee JDC]]
-	[[Category: ~~Armstrong, Z~~]]	+	[[Category: Davies GJ]]
-	[[Category: ~~Wong, C.S~~]]	+	[[Category: Florea BI]]
-	[[Category: ~~Kuo, C.L~~]]	+	[[Category: Kuo CL]]
-	[[Category: ~~Beenakker, T~~]]	+	[[Category: McGregor N]]
		+	[[Category: Offren WA]]
		+	[[Category: Overkleeft H]]
		+	[[Category: Wong CS]]

OCA at 05:08, 25 August 2021

OCA — Wed, 25 Aug 2021 05:08:00 GMT

←Older revision		Revision as of 05:08, 25 August 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7oms is ON HOLD	+	The entry 7oms is ON HOLD until Paper Publication

	Authors: McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H., Davies, G.J.		Authors: McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H., Davies, G.J.

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

OCA — Wed, 02 Jun 2021 13:38:34 GMT

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

←Older revision

Revision as of 13:38, 2 June 2021

OCA: New page: '''Unreleased structure''' The entry 7oms is ON HOLD Authors: McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B....

OCA — Wed, 02 Jun 2021 13:38:33 GMT

New page: '''Unreleased structure''' The entry 7oms is ON HOLD Authors: McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B....

New page

'''Unreleased structure'''

The entry 7oms is ON HOLD

Authors: McGregor, N., Beenakker, T., Kuo, C.L., Wong, C.S., Offren, W.A., Armstrong, Z., Codee, J.D.C., Aerts, J.M.F.G., Florea, B.I., Overkleeft, H., Davies, G.J.

Description: Bs164 in complex with mannocyclophellitol aziridine
[[Category: Unreleased Structures]]
[[Category: Florea, B.I]]
[[Category: Aerts, J.M.F.G]]
[[Category: Overkleeft, H]]
[[Category: Mcgregor, N]]
[[Category: Offren, W.A]]
[[Category: Codee, J.D.C]]
[[Category: Davies, G.J]]
[[Category: Armstrong, Z]]
[[Category: Wong, C.S]]
[[Category: Kuo, C.L]]
[[Category: Beenakker, T]]