6ha9
From Proteopedia
(Difference between revisions)
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| - | == | + | ==Structure of an endo-Xyloglucanase from Cellvibrio japonicus complexed with XXXG(2F)-beta-DNP== |
<StructureSection load='6ha9' size='340' side='right' caption='[[6ha9]], [[Resolution|resolution]] 2.00Å' scene=''> | <StructureSection load='6ha9' size='340' side='right' caption='[[6ha9]], [[Resolution|resolution]] 2.00Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[6ha9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HA9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6ha9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Celju Celju]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HA9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HA9 FirstGlance]. <br> |
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE'>NFG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NFG:2,4-DINITROPHENYL+2-DEOXY-2-FLUORO-BETA-D-GLUCOPYRANOSIDE'>NFG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=XYS:XYLOPYRANOSE'>XYS</scene></td></tr> | ||
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/ | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cel5D, CJA_3010 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=498211 CELJU])</td></tr> |
| + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Xyloglucan-specific_endo-beta-1,4-glucanase Xyloglucan-specific endo-beta-1,4-glucanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.151 3.2.1.151] </span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ha9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ha9 OCA], [http://pdbe.org/6ha9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ha9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ha9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ha9 ProSAT]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ha9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ha9 OCA], [http://pdbe.org/6ha9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ha9 RCSB], [http://www.ebi.ac.uk/pdbsum/6ha9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ha9 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Xyloglucan (XyG) is a complex polysaccharide that is ubiquitous and often abundant in the cell walls of terrestrial plants. XyG metabolism is therefore a key component of the global carbon cycle, and hence XyG enzymology is of significant fundamental and applied importance in biomass conversion. To facilitate structure-function analyses of XyG-specific endo-glucanases, we have synthesized a 2',4'-dinitrophenyl 2-deoxy-2-fluoro-beta-glycoside mechanism-based inhibitor based on the highly branched XyG repeating motif XXXG (Xyl3Glc4: ([alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1-->4)-[alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1 -->4)-[alpha-d-Xylp-(1-->6)]-beta-d-Glcp-(1-->4)-d-Glcp. Key steps in the chemo-enzymatic synthesis included selective enzyme hydrolysis of XyG polysaccharide to produce the core heptasaccharide, per-O-acetylation, alpha-bromination, reductive glycal formation, electrophilic fluorination, SNAr glycosylation, and Zemplen deprotection. The resulting compound, XXXG(2F)-beta-DNP, specifically labelled the active sites of several endo-(xylo)glucanases by accumulation of a covalent glycosyl-enzyme intermediate, as revealed by intact protein mass spectrometry. Crystallography of a complex with a Cellvibrio japonicus Glycoside Hydrolase Family 5 (GH5) endo-xyloglucanase corroborated the covalent nature of the intermediate, and further revealed the anticipated specificity for the catalytic nucleophile of this anomeric-configuration-retaining glycosidase. This specificity complements that of an analogous XXXG N-bromoacetylglycosylamine inhibitor, which labelled the catalytic acid-base sidechain in the same enzyme [Attia, et al., Biotechnol. Biofuels, 2018, 11, 45]. We anticipate that these inhibitors may find continued use in mechanistic analyses of endo-(xylo)glucanases from diverse GH families. | ||
| + | |||
| + | Synthesis and application of a highly branched, mechanism-based 2-deoxy-2-fluoro-oligosaccharide inhibitor of endo-xyloglucanases.,Jain N, Attia MA, Offen WA, Davies GJ, Brumer H Org Biomol Chem. 2018 Nov 21;16(45):8732-8741. doi: 10.1039/c8ob02250j. PMID:30387796<ref>PMID:30387796</ref> | ||
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| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 6ha9" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Celju]] |
| + | [[Category: Xyloglucan-specific endo-beta-1,4-glucanase]] | ||
[[Category: Davies, G J]] | [[Category: Davies, G J]] | ||
[[Category: Offen, W A]] | [[Category: Offen, W A]] | ||
Current revision
Structure of an endo-Xyloglucanase from Cellvibrio japonicus complexed with XXXG(2F)-beta-DNP
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