6zbx - Revision history

OCA at 13:46, 24 January 2024

OCA — Wed, 24 Jan 2024 13:46:12 GMT

←Older revision		Revision as of 13:46, 24 January 2024
Line 1:		Line 1:

-	====	+	==Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6- alpha-manno-cyclophellitol carbasugar-stabilised trisaccharide inhibitor==
-	<StructureSection load='6zbx' size='340' side='right'caption='[[6zbx]]' scene=''>	+	<StructureSection load='6zbx' size='340' side='right'caption='[[6zbx]], [[Resolution\|resolution]] 1.35Å' 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'>[[6zbx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Niallia_circulans Niallia circulans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6ZBX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ZBX 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=6zbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zbx OCA], [https://pdbe.org/6zbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zbx RCSB], [https://www.ebi.ac.uk/pdbsum/6zbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zbx 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]] 1.35Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=M96:(1~{S},2~{R},3~{S},4~{R},5~{R})-5-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol'>M96</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=PBW:(1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol'>PBW</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=6zbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zbx OCA], [https://pdbe.org/6zbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zbx RCSB], [https://www.ebi.ac.uk/pdbsum/6zbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zbx ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A6B9HEB8_NIACI A0A6B9HEB8_NIACI]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	There is a vast genomic resource for enzymes active on carbohydrates. Lagging far behind, however, are functional chemical tools for the rapid characterization of carbohydrate-active enzymes. Activity-based probes (ABPs) offer one chemical solution to these issues with ABPs based upon cyclophellitol epoxide and aziridine covalent and irreversible inhibitors representing a potent and widespread approach. Such inhibitors for enzymes active on polysaccharides are potentially limited by the requirement for several glycosidic bonds, themselves substrates for the enzyme targets. Here we show that non-hydrolysable trisaccharide can be synthesized and applied even to enzymes with challenging subsite requirements. We find that incorporation of carbasugar moieties, which we accomplished by cuprate-assisted regioselective trans-diaxial epoxide opening of carba-mannal we synthesised for this purpose, yields inactivators that act as powerful activity-based inhibitors for a-1,6 endo-mannanases. 3-D structures at 1.35 - 1.47 A resolutions confirm the design rationale and binding to the enzymatic nucleophile. Carbasugar oligosaccharide cyclophellitols offer a powerful new approach for the design of robust endoglycosidase inhibitors, while the synthesis procedures presented here should allow adaptation towards activity-based endoglycosidase probes as well as configurational isosteres targeting other endoglycosidase families.
		+
		+	The Development of Non-Hydrolysable Oligosaccharide Activity-Based Inactivators for Endoglycanases: A Case Study on a-1,6 Mannanases.,Overkleeft HS, Schroder S, Offen W, Males A, Jin Y, de Boer C, Enotarpi J, van der Marel G, Florea B, Codee J, Davies G Chemistry. 2021 Apr 20. doi: 10.1002/chem.202101255. PMID:33878235<ref>PMID:33878235</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6zbx" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Niallia circulans]]
		+	[[Category: Codee JDC]]
		+	[[Category: Davies GJ]]
		+	[[Category: De Boer C]]
		+	[[Category: Enoterpi J]]
		+	[[Category: Jin Y]]
		+	[[Category: Marino L]]
		+	[[Category: Offen WA]]
		+	[[Category: Overkleeft HS]]
		+	[[Category: Schroeder S]]
		+	[[Category: Van der Marel GA]]

OCA at 05:18, 28 April 2021

OCA — Wed, 28 Apr 2021 05:18:24 GMT

←Older revision		Revision as of 05:18, 28 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6zbx ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6zbx' size='340' side='right'caption='[[6zbx]]' scene=''>
-	~~Authors~~: ~~Schroeder, S~~.~~, Offen, W~~.A.~~, Jin, Y~~.~~, De Boer, C~~.~~, Enoterpi, J~~.~~, Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft, H.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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~: ~~STRUCTURE OF THE CATALYTIC DOMAIN OF BCGH76 IN COMPLEX WITH A 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=6zbx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6zbx OCA], [https://pdbe.org/6zbx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6zbx RCSB], [https://www.ebi.ac.uk/pdbsum/6zbx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6zbx ProSAT]</span></td></tr>
-	[~~[Category~~: ~~Unreleased Structures~~]]	+	</table>
-	~~[[Category: Van Der Marel~~, ~~G.A]]~~	+	__TOC__
-	[~~[Category~~: ~~Codee, J~~.D.C]]	+	</StructureSection>
-	~~[[Category: Marino~~, ~~L]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Offen, W~~.A]]	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Overkleeft, H~~.S]]	+
-	~~[[Category: Schroeder~~, ~~S]]~~	+
-	[~~[Category~~: ~~Davies, G~~.J]]	+
-	[~~[Category~~: ~~Jin, Y]~~]	+
-	[[Category: ~~De Boer, C~~]]	+
-	[[Category: ~~Enoterpi, J~~]]	+

OCA at 07:52, 22 July 2020

OCA — Wed, 22 Jul 2020 07:52:19 GMT

←Older revision		Revision as of 07:52, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Schroeder, S., Offen, W.A., Jin, Y., De Boer, C., Enoterpi, J., Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft, H.S., Davies, G.J.		Authors: Schroeder, S., Offen, W.A., Jin, Y., De Boer, C., Enoterpi, J., Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft, H.S., Davies, G.J.

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

OCA — Wed, 17 Jun 2020 08:55:09 GMT

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

←Older revision

Revision as of 08:55, 17 June 2020

OCA: New page: '''Unreleased structure''' The entry 6zbx is ON HOLD Authors: Schroeder, S., Offen, W.A., Jin, Y., De Boer, C., Enoterpi, J., Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft,...

OCA — Wed, 17 Jun 2020 08:55:07 GMT

New page: '''Unreleased structure''' The entry 6zbx is ON HOLD Authors: Schroeder, S., Offen, W.A., Jin, Y., De Boer, C., Enoterpi, J., Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft,...

New page

'''Unreleased structure'''

The entry 6zbx is ON HOLD

Authors: Schroeder, S., Offen, W.A., Jin, Y., De Boer, C., Enoterpi, J., Marino, L., van der Marel, G.A., Codee, J.D.C., Overkleeft, H.S., Davies, G.J.

Description: STRUCTURE OF THE CATALYTIC DOMAIN OF BCGH76 IN COMPLEX WITH A COVALENT INHIBITOR
[[Category: Unreleased Structures]]
[[Category: Van Der Marel, G.A]]
[[Category: Codee, J.D.C]]
[[Category: Marino, L]]
[[Category: Offen, W.A]]
[[Category: Overkleeft, H.S]]
[[Category: Schroeder, S]]
[[Category: Davies, G.J]]
[[Category: Jin, Y]]
[[Category: De Boer, C]]
[[Category: Enoterpi, J]]