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

Structure. 1999 Jul 15;7(7):853-64. doi: 10.1016/s0969-2126(99)80108-7.


Background: Many enzymes that digest polysaccharides contain separate polysaccharide-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 fimi xylanase D is shown to bind xylan but not cellulose. Its structure is similar 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 xylan-binding site is a groove made from two tryptophan residues that stack against the faces of the sugar rings, plus several hydrogen-bonding polar residues.

Conclusions: The biggest difference between the family IIa and IIb domains is that in the former the solvent-exposed tryptophan sidechains are coplanar, whereas in the latter they are perpendicular, forming a twisted binding site. The binding sites are therefore complementary to the secondary structures of the ligands cellulose and xylan. XBD1 and CexCBD represent a striking example of two proteins that have high sequence similarity but a different function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Cellulose / metabolism*
  • Crystallography, X-Ray
  • DNA Primers
  • Endo-1,4-beta Xylanases
  • Ligands
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Protein Structure, Secondary
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Thermodynamics
  • Xylans / metabolism*
  • Xylosidases / chemistry*
  • Xylosidases / metabolism
  • beta-Glucosidase / chemistry*
  • beta-Glucosidase / metabolism


  • DNA Primers
  • Ligands
  • Xylans
  • Cellulose
  • Xylosidases
  • beta-Glucosidase
  • Endo-1,4-beta Xylanases

Associated data

  • PDB/1XBD
  • PDB/2XBD