Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules

Montanier, Cedric and Flint, James E. and Bolam, David N. and Xie, Hefang and Liu, Ziyuan and Rogowski, Artur and Weiner, David P. and Ratnaparkhe, Supriya and Nurizzo, Didier and Roberts, Shirley M. and Turkenburg, Johan P. and Davies, Gideon J. and Gilbert, Harry J. (2010) Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. The Journal of Biological Chemistry, 285 (41). pp. 31742-31754. ISSN 0021-9258

Full content URL: http://dx.doi.org/10.1074/jbc.M110.142133

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Item Type:Article
Item Status:Live Archive

Abstract

The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

Keywords:Biochemical properties, Biological process, Carbohydrate binding modules, Carbohydrate recognition, Circular permutation, Galactans, Hydrophobic interactions, Ligand binding, Ligand recognition, Ligand specificity, Ligand-binding sites, Non-catalytic, Plant cell wall, Polar interactions, Protein dimerization, Sequence alignments, Three-dimensional structure, Xylanases, Binding energy, Binding sites, Gene transfer, Hydrophobicity, Ligands, Organic compounds, Plant cell culture, Polysaccharides, Proteins, Sugar (sucrose), Crystal structure, calcium, carbohydrate binding module family 36, carbohydrate binding module family 60, carbohydrate binding protein, cellulose, galactan, unclassified drug, xylan, amino terminal sequence, article, beta sheet, binding affinity, carboxy terminal sequence, cell wall, controlled study, crystal structure, dimerization, enthalpy, entropy, hydrolysis, in vitro study, molecular evolution, molecular recognition, nonhuman, nucleotide sequence, phloem, priority journal, protein localization, sequence alignment, wild type, xylem, Binding Sites, Calcium, Cellvibrio, Crystallography, X-Ray, Evolution, Molecular, Protein Multimerization, Protein Structure, Quaternary, Protein Structure, Secondary, Substrate Specificity, Xylosidases
Subjects:C Biological Sciences > C720 Biological Chemistry
C Biological Sciences > C110 Applied Biology
Divisions:College of Science > School of Life Sciences
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ID Code:12457
Deposited On:13 Dec 2013 12:00

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