The crystal structure of the family GH-51 a-L-arabinofuranosidase from T. xylanilyticus has been solved as a seleno-methionyl derivative and as an inactive mutant Glu176Gln in complex with a branched pentasaccharide. The overall structure shows the two characteristic GH-51 domains: a catalytic domain that is folded into a (α/β)8-barrel and a C-terminal domain that displays jelly-roll architecture. The pentasaccharide is bound in a groove on the surface of the enzyme, with the mono arabinosyl-branch entering a tight pocket harbouring the catalytic dyad. Detailed analyses of both structures and comparisons with the two previously determined structures from G. stearothermophilus and C. thermocellum reveal important details unique to the T. xylanilyticus enzyme. In the absence of substrate, the enzyme adopts an open conformation. In the substrate-bound form, the loop connecting β-strand 2 to α-helix 2 closes the active site and interacts with the substrate through residues His98 and Trp99. The results of kinetic and fluorescence titration studies using mutants underline the importance of this loop, and support the notion of an interaction between Trp99 and the bound substrate. We suggest that the changes in loop conformation are an integral part of the T. xylanilyticus a-L-arabinofuranosidase reaction mechanism, and ensure efficient binding and release of substrate