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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 DOI10.2210/pdb6fwi/pdb
Related6FWG 6FWJ 6FWL 6FWM 6FWO 6FWP 6FWQ
DescriptorGlycosyl 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 Keywordshydrolase
Biological sourceBacteroides xylanisolvens XB1A
Total number of polymer chains1
Total formula weight44509.11
Authors
Primary citationSobala, 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: 32490192
DOI: 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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