6yqh - Revision history

OCA at 13:33, 24 January 2024

OCA — Wed, 24 Jan 2024 13:33:26 GMT

←Older revision		Revision as of 13:33, 24 January 2024
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	==GH146 beta-L-arabinofuranosidase bound to covalent inhibitor==		==GH146 beta-L-arabinofuranosidase bound to covalent inhibitor==
-	<StructureSection load='6yqh' size='340' side='right'caption='[[6yqh]]' scene=''>	+	<StructureSection load='6yqh' size='340' side='right'caption='[[6yqh]], [[Resolution\|resolution]] 1.41Å' 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=6YQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yqh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacteroides_thetaiotaomicron_VPI-5482 Bacteroides thetaiotaomicron VPI-5482]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQH 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=6yqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqh OCA], [https://pdbe.org/6yqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqh RCSB], [https://www.ebi.ac.uk/pdbsum/6yqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqh 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]] 1.41Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MES:2-(N-MORPHOLINO)-ETHANESULFONIC+ACID'>MES</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene>, <scene name='pdbligand=PJ5:(1~{S},2~{S},3~{S},4~{S})-4-(hydroxymethyl)cyclopentane-1,2,3-triol'>PJ5</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6yqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqh OCA], [https://pdbe.org/6yqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqh RCSB], [https://www.ebi.ac.uk/pdbsum/6yqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqh ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8AAW3_BACTN Q8AAW3_BACTN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The recent discovery of zinc-dependent retaining glycoside hydrolases (GHs), with active sites built around a Zn(Cys)(3) (Glu) coordination complex, has presented unresolved mechanistic questions. In particular, the proposed mechanism, depending on a Zn-coordinated cysteine nucleophile and passing through a thioglycosyl enzyme intermediate, remains controversial. This is primarily due to the expected stability of the intermediate C-S bond. To facilitate the study of this atypical mechanism, we report the synthesis of a cyclophellitol-derived beta-l-arabinofuranosidase inhibitor, hypothesised to react with the catalytic nucleophile to form a non-hydrolysable adduct analogous to the mechanistic covalent intermediate. This beta-l-arabinofuranosidase inhibitor reacts exclusively with the proposed cysteine thiol catalytic nucleophiles of representatives of GH families 127 and 146. X-ray crystal structures determined for the resulting adducts enable MD and QM/MM simulations, which provide insight into the mechanism of thioglycosyl enzyme intermediate breakdown. Leveraging the unique chemistry of cyclophellitol derivatives, the structures and simulations presented here support the assignment of a zinc-coordinated cysteine as the catalytic nucleophile and illuminate the finely tuned energetics of this remarkable metalloenzyme clan.
		+
		+	Cysteine Nucleophiles in Glycosidase Catalysis: Application of a Covalent beta-l-Arabinofuranosidase Inhibitor.,McGregor NGS, Coines J, Borlandelli V, Amaki S, Artola M, Nin-Hill A, Linzel D, Yamada C, Arakawa T, Ishiwata A, Ito Y, van der Marel GA, Codee JDC, Fushinobu S, Overkleeft HS, Rovira C, Davies GJ Angew Chem Int Ed Engl. 2021 Mar 8;60(11):5754-5758. doi: 10.1002/anie.202013920. , Epub 2021 Feb 2. PMID:33528085<ref>PMID:33528085</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yqh" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacteroides thetaiotaomicron VPI-5482]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Davies GJ]]		[[Category: Davies GJ]]
	[[Category: McGregor NGS]]		[[Category: McGregor NGS]]

OCA at 07:55, 27 January 2021

OCA — Wed, 27 Jan 2021 07:55:45 GMT

←Older revision		Revision as of 07:55, 27 January 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 6yqh ~~is ON HOLD until Paper Publication~~	+	==GH146 beta-L-arabinofuranosidase bound to covalent inhibitor==
-		+	<StructureSection load='6yqh' size='340' side='right'caption='[[6yqh]]' scene=''>
-	~~Authors~~: ~~McGregor~~, N.G.S., ~~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=6YQH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YQH FirstGlance]. <br>
-	~~Description~~: ~~GH146 beta~~-~~L-arabinofuranosidase bound to covalent inhibitor~~	+	</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=6yqh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yqh OCA], [https://pdbe.org/6yqh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yqh RCSB], [https://www.ebi.ac.uk/pdbsum/6yqh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yqh ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Mcgregor, N.G.S~~]]	+	__TOC__
-	[[Category: ~~Davies, G.J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Davies GJ]]
		+	[[Category: McGregor NGS]]

OCA at 04:13, 13 May 2020

OCA — Wed, 13 May 2020 04:13:27 GMT

←Older revision		Revision as of 04:13, 13 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yqh is ON HOLD	+	The entry 6yqh is ON HOLD until Paper Publication

	Authors: McGregor, N.G.S., Davies, G.J.		Authors: McGregor, N.G.S., Davies, G.J.
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	Description: GH146 beta-L-arabinofuranosidase bound to covalent inhibitor		Description: GH146 beta-L-arabinofuranosidase bound to covalent inhibitor
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Davies, G.J]]
	[[Category: Mcgregor, N.G.S]]		[[Category: Mcgregor, N.G.S]]
		+	[[Category: Davies, G.J]]

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

OCA — Wed, 22 Apr 2020 04:34:00 GMT

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

←Older revision

Revision as of 04:34, 22 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yqh is ON HOLD Authors: McGregor, N.G.S., Davies, G.J. Description: GH146 beta-L-arabinofuranosidase bound to covalent inhibitor [[Category: Unrel...

OCA — Wed, 22 Apr 2020 04:33:59 GMT

New page: '''Unreleased structure''' The entry 6yqh is ON HOLD Authors: McGregor, N.G.S., Davies, G.J. Description: GH146 beta-L-arabinofuranosidase bound to covalent inhibitor [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 6yqh is ON HOLD

Authors: McGregor, N.G.S., Davies, G.J.

Description: GH146 beta-L-arabinofuranosidase bound to covalent inhibitor
[[Category: Unreleased Structures]]
[[Category: Davies, G.J]]
[[Category: Mcgregor, N.G.S]]