1PZ2

Crystal structure of a transient covalent reaction intermediate of a family 51 alpha-L-arabinofuranosidase

Summary for 1PZ2

• Entry DOI: 10.2210/pdb1pz2/pdb
• Related: 1PZ3 1QW8 1QW9
• Descriptor: Alpha-L-arabinofuranosidase, alpha-L-arabinofuranose (3 entities in total)
• Functional Keywords: beta-alpha8-barrel, hydrolase
• Biological source: Geobacillus stearothermophilus
• Cellular location: Cytoplasm : Q9XBQ3
• Total number of polymer chains: 2
• Total formula weight: 114753.99

Authors

Hoevel, K.,Shallom, D.,Niefind, K.,Belakhov, V.,Shoham, G.,Baasov, T.,Shoham, Y.,Schomburg, D. (deposition date: 2003-07-09, release date: 2003-10-07, Last modification date: 2024-10-09)

Primary citation

Hoevel, K.,Shallom, D.,Niefind, K.,Belakhov, V.,Shoham, G.,Baasov, T.,Shoham, Y.,Schomburg, D.
Crystal structure and snapshots along the reaction pathway of a family 51 alpha-L-arabinofuranosidase
Embo J., 22:4922-4932, 2003

PubMed Abstract: High-resolution crystal structures of alpha-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 (beta/alpha)8-barrel and a 12-stranded beta 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 A 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 A electrophilic migration of the anomeric carbon takes place during the hydrolysis.

PubMed: 14517232
DOI: 10.1093/emboj/cdg494

Experimental method

X-RAY DIFFRACTION (2 Å)