7nl5: Difference between revisions

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<StructureSection load='7nl5' size='340' side='right'caption='[[7nl5]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='7nl5' size='340' side='right'caption='[[7nl5]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7nl5]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NL5 FirstGlance]. <br>
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NL5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NL5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=UKQ:(1R,6S)-5beta-(Hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2beta,3beta,4alpha-triol'>UKQ</scene>, <scene name='pdbligand=UKT:(1R,2R,3R,4S,5R)-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol'>UKT</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene></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]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=UKQ:(1R,6S)-5beta-(Hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2beta,3beta,4alpha-triol'>UKQ</scene>, <scene name='pdbligand=UKT:(1R,2R,3R,4S,5R)-4-(hydroxymethyl)cyclohexane-1,2,3,5-tetrol'>UKT</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=7nl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nl5 OCA], [https://pdbe.org/7nl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nl5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nl5 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=7nl5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nl5 OCA], [https://pdbe.org/7nl5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nl5 RCSB], [https://www.ebi.ac.uk/pdbsum/7nl5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nl5 ProSAT]</span></td></tr>
</table>
</table>
<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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7nl5" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Boer, C De]]
[[Category: Codee JDC]]
[[Category: Codee, J D.C]]
[[Category: Davies GJ]]
[[Category: Davies, G J]]
[[Category: De Boer C]]
[[Category: Enotarpi, J]]
[[Category: Enotarpi J]]
[[Category: Florea, B I]]
[[Category: Florea BI]]
[[Category: Jin, Y]]
[[Category: Jin Y]]
[[Category: Males, A]]
[[Category: Males A]]
[[Category: Marel, G A.van der]]
[[Category: Marino L]]
[[Category: Marino, L]]
[[Category: Offen WA]]
[[Category: Offen, W A]]
[[Category: Overkleeft HS]]
[[Category: Overkleeft, H S]]
[[Category: Schroeder S]]
[[Category: Schroeder, S]]
[[Category: Van der Marel GA]]
[[Category: Cyclophellitol]]
[[Category: Epoxide]]
[[Category: Hydrolase]]
[[Category: Mannanase]]

Latest revision as of 12:00, 17 October 2024

Structure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitorStructure of the catalytic domain of the Bacillus circulans alpha-1,6 Mannanase in complex with an alpha-1,6-alpha-manno-cyclophellitol trisaccharide inhibitor

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

7nl5, resolution 1.40Å

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OCA
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