6fwm | pdb_00006fwm

Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-1,2-anhydro-mannose hydrolyzed by enzyme

spinqualitylabelsall models 6fwm, resolution 1.28Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6fwm is a 1 chain structure with sequence from Bacteroides sp. xb1a. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, GLC, M96 Gene: BXY_34140 (Bacteroides sp. XB1A) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-alpha-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol beta-1,2-aziridine and beta-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope (E 3) conformation. Kinetic isotope effects (k cat/K M) for anomeric-(2)H and anomeric-(13)C support an oxocarbenium ion-like transition state, and that for C2-(18)O (1.052 +/- 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism. An Epoxide Intermediate in Glycosidase Catalysis.,Sobala LF, Speciale G, Zhu S, Raich L, Sannikova N, Thompson AJ, Hakki Z, Lu D, Shamsi Kazem Abadi S, Lewis AR, Rojas-Cervellera V, Bernardo-Seisdedos G, Zhang Y, Millet O, Jimenez-Barbero J, Bennet AJ, Sollogoub M, Rovira C, Davies GJ, Williams SJ ACS Cent Sci. 2020 May 27;6(5):760-770. doi: 10.1021/acscentsci.0c00111. Epub, 2020 Apr 16. PMID:32490192 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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