title: The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved.
abstract: 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 A. The protein is a beta-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.
authors.affiliation: Laboratoire d'Architecture et de Fonction des Macromolécules Biologiques, IBSM, CNRS Marseille and University Aix-Marseille I & II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France. czjzek@afmb.cnrs-mrs.fr
authors.forename: M
authors.initials: M
authors.lastname: Czjzek
authors.forename: D N
authors.initials: DN
authors.lastname: Bolam
authors.forename: A
authors.initials: A
authors.lastname: Mosbah
authors.forename: J
authors.initials: J
authors.lastname: Allouch
authors.forename: C M
authors.initials: CM
authors.lastname: Fontes
authors.forename: L M
authors.initials: LM
authors.lastname: Ferreira
authors.forename: O
authors.initials: O
authors.lastname: Bornet
authors.forename: V
authors.initials: V
authors.lastname: Zamboni
authors.forename: H
authors.initials: H
authors.lastname: Darbon
authors.forename: N L
authors.initials: NL
authors.lastname: Smith
authors.forename: G W
authors.initials: GW
authors.lastname: Black
authors.forename: B
authors.initials: B
authors.lastname: Henrissat
authors.forename: H J
authors.initials: HJ
authors.lastname: Gilbert
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D050260:Carbohydrate Metabolism; D018360:Crystallography, X-Ray; D008024:Ligands; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017386:Sequence Homology, Amino Acid; D013329:Structure-Activity Relationship; D043325:Xylan Endo-1,3-beta-Xylosidase; D014995:Xylosidases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D008024:Ligands; D014995:Xylosidases; D043325:Xylan Endo-1,3-beta-Xylosidase