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5m7y
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 5m7y is ON HOLD Authors: Males, A., Alonso-Gil, S., Fernandes, P., Williams, S.J., Rovira, C., Davies, G.J. Description: Crystal structure of GH125...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannotriose== | |
| + | <StructureSection load='5m7y' size='340' side='right'caption='[[5m7y]], [[Resolution|resolution]] 1.55Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[5m7y]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_perfringens_str._13 Clostridium perfringens str. 13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5M7Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5M7Y FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.55Å</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=MG:MAGNESIUM+ION'>MG</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=5m7y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5m7y OCA], [https://pdbe.org/5m7y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5m7y RCSB], [https://www.ebi.ac.uk/pdbsum/5m7y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5m7y ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/Q8XNB2_CLOPE Q8XNB2_CLOPE] | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Conformational analysis of enzyme-catalyzed mannoside hydrolysis has revealed two predominant conformational itineraries through B2,5 or 3H4 transition-state (TS) conformations. A prominent unassigned catalytic itinerary is that of exo-1,6-alpha-mannosidases belonging to CAZy family 125. A published complex of Clostridium perfringens GH125 enzyme with a nonhydrolyzable 1,6-alpha-thiomannoside substrate mimic bound across the active site revealed an undistorted 4C1 conformation and provided no insight into the catalytic pathway of this enzyme. We show through a purely computational approach (QM/MM metadynamics) that sulfur-for-oxygen substitution in the glycosidic linkage fundamentally alters the energetically accessible conformational space of a thiomannoside when bound within the GH125 active site. Modeling of the conformational free energy landscape (FEL) of a thioglycoside strongly favors a mechanistically uninformative 4C1 conformation within the GH125 enzyme active site, but the FEL of corresponding O-glycoside substrate reveals a preference for a Michaelis complex in an OS2 conformation (consistent with catalysis through a B2,5 TS). This prediction was tested experimentally by determination of the 3D X-ray structure of the pseudo-Michaelis complex of an inactive (D220N) variant of C. perfringens GH125 enzyme in complex with 1,6-alpha-mannobiose. This complex revealed unambiguous distortion of the -1 subsite mannoside to an OS2 conformation, matching that predicted by theory and supporting an OS2 --> B2,5 --> 1S5 conformational itinerary for GH125 alpha-mannosidases. This work highlights the power of the QM/MM approach and identified shortcomings in the use of nonhydrolyzable substrate analogues for conformational analysis of enzyme-bound species. | ||
| - | + | Computational Design of Experiment Unveils the Conformational Reaction Coordinate of GH125 alpha-Mannosidases.,Alonso-Gil S, Males A, Fernandes PZ, Williams SJ, Davies GJ, Rovira C J Am Chem Soc. 2017 Jan 3. doi: 10.1021/jacs.6b11247. PMID:28026180<ref>PMID:28026180</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | [[Category: | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 5m7y" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: | + | ==See Also== |
| - | [[Category: | + | *[[Mannosidase 3D structures|Mannosidase 3D structures]] |
| - | [[Category: | + | == References == |
| - | [[Category: | + | <references/> |
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Clostridium perfringens str. 13]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Alonso-Gil S]] | ||
| + | [[Category: Davies GJ]] | ||
| + | [[Category: Fernandes P]] | ||
| + | [[Category: Males A]] | ||
| + | [[Category: Rovira C]] | ||
| + | [[Category: Williams SJ]] | ||
Current revision
Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannotriose
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