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Crystal structure and snapshots along the reaction pathway of a family 51 α‐ L ‐arabinofuranosidase
Author(s) -
Hövel Klaus,
Shallom Dalia,
Niefind Karsten,
Belakhov Valery,
Shoham Gil,
Baasov Timor,
Shoham Yuval,
Schomburg Dietmar
Publication year - 2003
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/cdg494
Subject(s) - random hexamer , stereochemistry , oxocarbenium , hydrogen bond , anomer , crystallography , biology , catalysis , chemistry , nucleophile , biochemistry , molecule , organic chemistry
High‐resolution crystal structures of α‐ L ‐arabinofuranosidase from Geobacillus stearothermophilus T‐6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (β/α) 8 ‐barrel and a 12‐stranded β sandwich with jelly‐roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl—enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 Å apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion‐like transition state via charge delocalization and specific protein—substrate interactions. The enzyme is an anti ‐protonator, and a 1.7 Å electrophilic migration of the anomeric carbon takes place during the hydrolysis.