6FWI
Structure of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-Glc-1,3-(1,2-anhydro-carba-mannosamine)
Summary for 6FWI
Entry DOI | 10.2210/pdb6fwi/pdb |
Related | 6FWG 6FWJ 6FWL 6FWM 6FWO 6FWP 6FWQ |
Descriptor | Glycosyl hydrolase family 71, ACETATE ION, (1~{R},2~{R},3~{R},4~{R},6~{R})-4-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3-diol, ... (5 entities in total) |
Functional Keywords | hydrolase |
Biological source | Bacteroides xylanisolvens XB1A |
Total number of polymer chains | 1 |
Total formula weight | 44509.11 |
Authors | Sobala, L.F.,Speciale, G.,Hakki, Z.,Fernandes, P.Z.,Raich, L.,Rojas-Cervellera, V.,Bennet, A.,Thompson, A.J.,Bernardo-Seisdedos, G.,Millet, O.,Zhu, S.,Lu, D.,Sollogoub, M.,Rovira, C.,Jimenez-Barbero, J.,Davies, G.J.,Williams, S.J. (deposition date: 2018-03-06, release date: 2019-09-18, Last modification date: 2024-01-17) |
Primary citation | Sobala, L.F.,Speciale, G.,Zhu, S.,Raich, L.,Sannikova, N.,Thompson, A.J.,Hakki, Z.,Lu, D.,Shamsi Kazem Abadi, S.,Lewis, A.R.,Rojas-Cervellera, V.,Bernardo-Seisdedos, G.,Zhang, Y.,Millet, O.,Jimenez-Barbero, J.,Bennet, A.J.,Sollogoub, M.,Rovira, C.,Davies, G.J.,Williams, S.J. An Epoxide Intermediate in Glycosidase Catalysis. Acs Cent.Sci., 6:760-770, 2020 Cited by PubMed Abstract: 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 -α-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 β-1,2-aziridine and β-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 ( ) conformation. Kinetic isotope effects ( / ) for anomeric-H and anomeric-C support an oxocarbenium ion-like transition state, and that for C2-O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism. PubMed: 32490192DOI: 10.1021/acscentsci.0c00111 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (1.25 Å) |
Structure validation
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