3akf | pdb_00003akf
Crystal structure of exo-1,5-alpha-L-arabinofuranosidase
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedExo-1,5-alpha-L-arabinofuranosidases belonging to glycoside hydrolase family 43 have strict substrate specificity. These enzymes hydrolyze only the alpha-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-alpha-L-arabinofuranosidase. The catalytic module is composed of a 5-bladed beta-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 beta-trefoil-fold. A sugar complex structure with alpha-1,5-L-arabinofuranotriose revealed three subsites in the catalytic domain, and a sugar complex structure with alpha-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. 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.,Fujimoto Z, Ichinose H, Maehara T, Honda M, Kitaoka M, Kaneko S J Biol Chem. 2010 Oct 29;285(44):34134-43. Epub 2010 Aug 25. PMID:20739278[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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