The Location of the Ligand-binding Site of Carbohydrate-binding Modules That Have Evolved from a Common Sequence Is Not Conserved

• Published in: The Journal of biological chemistry Vol. 276; no. 51; pp. 48580 - 48587
• Main Authors: Czjzek, Mirjam, Bolam, David N., Mosbah, Amor, Allouch, Julie, Fontes, Carlos M.G.A., Ferreira, Luis M.A., Bornet, Olivier, Zamboni, Véronique, Darbon, Hervé, Smith, Nicola L., Black, Gary W., Henrissat, Bernard, Gilbert, Harry J.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.12.2001; American Society for Biochemistry and Molecular Biology
• Subjects: Amino Acid Sequence; Binding Sites; Carbohydrate Metabolism; Clostridium thermocellum; Crystallography, X-Ray; Ligands; Models, Molecular; Molecular Sequence Data; Polysaccharides; Sequence Homology, Amino Acid; Structure-Activity Relationship; Xylan Endo-1,3-beta-Xylosidase; xylans; Xylosidases - chemistry; Xylosidases - metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M109142200

Polysaccharide-degrading enzymes are generally modular proteins that contain non-catalytic carbohydrate-binding modules (CBMs), which potentiate the activity of the catalytic module. CBMs have been grouped into sequence-based families, and three-dimensional structural data are available for half of these families. Clostridium thermocellum xylanase 11A is a modular enzyme that contains a CBM from family 6 (CBM6), for which no structural data are available. We have determined the crystal structure of this module to a resolution of 2.1 Å. The protein is a β-sandwich that contains two potential ligand-binding clefts designated cleft A and B. The CBM interacts primarily with xylan, and NMR spectroscopy coupled with site-directed mutagenesis identified cleft A, containing Trp-92, Tyr-34, and Asn-120, as the ligand-binding site. The overall fold of CBM6 is similar to proteins in CBM families 4 and 22, although surprisingly the ligand-binding site in CBM4 and CBM22 is equivalent to cleft B in CBM6. These structural data define a superfamily of CBMs, comprising CBM4, CBM6, and CBM22, and demonstrate that, although CBMs have evolved from a relatively small number of ancestors, the structural elements involved in ligand recognition have been assembled at different locations on the ancestral scaffold.