A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity

Background: Many enzymes that digest polysaccharides contain separate polys accharide-binding domains. Structures have been previously determined for a number of cellulose-binding domains (CBDs) from cellulases. Results: The family IIb xylan-binding domain 1 (XBD1) from Cellulomonas fim i xylanase D is shown to bind xylan but not cellulose. Its structure is sim ilar to that of the homologous family IIa CBD from C, fimi Cex, consisting of two four-stranded beta sheets that form a twisted 'beta sandwich'. The x ylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar r esidues. Conclusions: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplana r, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary struct ures of the ligands cellulose and xylan. XBD1 and Cex(CBD) represent a stri king example of two proteins that have high sequence similarity but a diffe rent function.