3AKI

Crystal structure of exo-1,5-alpha-L-arabinofuranosidase complexed with alpha-L-arabinofuranosyl azido

Summary for 3AKI

• Entry DOI: 10.2210/pdb3aki/pdb
• Related: 3AKF 3AKG 3AKH
• Descriptor: Putative secreted alpha L-arabinofuranosidase II, CHLORIDE ION, SODIUM ION, ... (6 entities in total)
• Functional Keywords: five-bladed beta propeller, beta-trefoil, hydrolase
• Biological source: Streptomyces avermitilis
• Total number of polymer chains: 1
• Total formula weight: 52788.45

Authors

Fujimoto, Z.,Ichinose, H.,Kaneko, S. (deposition date: 2010-07-14, release date: 2010-08-25, Last modification date: 2023-11-01)

Primary citation

Fujimoto, Z.,Ichinose, H.,Maehara, T.,Honda, M.,Kitaoka, M.,Kaneko, S.
Crystal Structure of an Exo-1,5-{alpha}-L-arabinofuranosidase from Streptomyces avermitilis Provides Insights into the Mechanism of Substrate Discrimination between Exo- and Endo-type Enzymes in Glycoside Hydrolase Family 43.
J.Biol.Chem., 285:34134-34143, 2010

PubMed Abstract: Exo-1,5-α-L-arabinofuranosidases belonging to glycoside hydrolase family 43 have strict substrate specificity. These enzymes hydrolyze only the α-1,5-linkages of linear arabinan and arabino-oligosaccharides in an exo-acting manner. The enzyme from Streptomyces avermitilis contains a core catalytic domain belonging to glycoside hydrolase family 43 and a C-terminal arabinan binding module belonging to carbohydrate binding module family 42. We determined the crystal structure of intact exo-1,5-α-L-arabinofuranosidase. The catalytic module is composed of a 5-bladed β-propeller topologically identical to the other family 43 enzymes. The arabinan binding module had three similar subdomains assembled against one another around a pseudo-3-fold axis, forming a β-trefoil-fold. A sugar complex structure with α-1,5-L-arabinofuranotriose revealed three subsites in the catalytic domain, and a sugar complex structure with α-L-arabinofuranosyl azide revealed three arabinose-binding sites in the carbohydrate binding module. A mutagenesis study revealed that substrate specificity was regulated by residues Asn-159, Tyr-192, and Leu-289 located at the aglycon side of the substrate-binding pocket. The exo-acting manner of the enzyme was attributed to the strict pocket structure of subsite -1, formed by the flexible loop region Tyr-281-Arg-294 and the side chain of Tyr-40, which occupied the positions corresponding to the catalytic glycon cleft of GH43 endo-acting enzymes.

PubMed: 20739278
DOI: 10.1074/jbc.M110.164251

Experimental method

X-RAY DIFFRACTION (2 Å)