5m7i | pdb_00005m7i

Crystal structure of GH125 1,6-alpha-mannosidase mutant from Clostridium perfringens in complex with 1,6-alpha-mannobiose

spinqualitylabelsall models 5m7i, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5m7i is a 1 chain structure with sequence from Clope. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: BMA, MAN Gene: CPE0426 (CLOPE) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Mannosidase 3D structures

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