Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to β-cyclodextrin

Sorimachi, Kay; Gal-Coeffet, M.-F. Le; Williamson, Gary; Archer, David B.; Williamson, Michael P.

doi:10.1016/s0969-2126(97)00220-7

Cited by 184 publications

(217 citation statements)

References 59 publications

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“…The stoichiometry of binding for all oligosaccharides was 1:1, indicating that there is only one ligand-binding site per protein molecule. This is consistent with the other CBMs, such as CBM4 (4), CBM9 (36), and CBM22 (13), which also contain single carbohydrate-binding sites, but is in contrast to the starch-binding modules that can interact with two amylose chains (37). These data suggest that the CBM6 from C. thermocellum Xyn11A is primarily a xylan-binding module.…”

Section: Resultssupporting

confidence: 85%

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

Czjzek

Bolam

Mosbah

et al. 2001

Journal of Biological Chemistry

108

113

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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 ␤-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.

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Section: Resultssupporting

confidence: 85%

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

Czjzek

Bolam

Mosbah

et al. 2001

Journal of Biological Chemistry

108

113

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“…Although many of these modules target components of the plant cell wall, several CBM families contain proteins that bind to insoluble storage polysaccharides such as starch and glycogen. Indeed, the structure and biochemistry of several family 20 CBMs, which bind to starch, have been analysed extensively (see [6][7][8][9][10][11][12][13] for examples). Furthermore, numerous crystal structures of starch-modifying enzymes have revealed malto-oligosaccharide-binding sites that are distinct from the substrate-binding cleft, indicating that these enzymes also contain starch-binding CBMs [14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

“…These were the well-known plant-derived lectins ricin toxin B-chain [19] and WGA (wheat germ agglutinin) [20]. The structure of a family 20 starch-binding module in complex with β-cyclodextrin was determined by NMR spectroscopy [9]. Since the beginning of 2001, however, the structures of 15 CBMs, derived from ten different families, have been determined in complex with their oligosaccharide ligands derived both from the three major plant cell-wall polysaccharides, cellulose, xylan and mannan, as well as β-1,3-glucan and starch.…”

Section: Introductionmentioning

confidence: 99%

Carbohydrate-binding modules: fine-tuning polysaccharide recognition

Boraston

Bolam

Gilbert

et al. 2004

Biochemical Journal

1,777

1,724

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The enzymic degradation of insoluble polysaccharides is one of the most important reactions on earth. Despite this, glycoside hydrolases attack such polysaccharides relatively inefficiently as their target glycosidic bonds are often inaccessible to the active site of the appropriate enzymes. In order to overcome these problems, many of the glycoside hydrolases that utilize insoluble substrates are modular, comprising catalytic modules appended to one or more non-catalytic CBMs (carbohydrate-binding modules). CBMs promote the association of the enzyme with the substrate. In view of the central role that CBMs play in the enzymic hydrolysis of plant structural and storage polysaccharides, the ligand specificity displayed by these protein modules and the mechanism by which they recognize their target carbohydrates have received considerable attention since their discovery almost 20 years ago. In the last few years, CBM research has harnessed structural, functional and bioinformatic approaches to elucidate the molecular determinants that drive CBM-carbohydrate recognition. The present review summarizes the impact structural biology has had on our understanding of the mechanisms by which CBMs bind to their target ligands.

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“…2A). Laf-CBM homology model was docked inside the SAXS density, and the position of ␣-cD was determined by superimposing laf-CBM to the structure of the Aspergillus niger CBM20 bound to ␤-cD (Protein Data Bank code 1ACZ) (41). The composite laf-CBM model bound to ␣-cD was then refined against the SAXS envelope using low resolution real space refinement.…”

Section: Saxs-restrained Model Of Laforin Cbm Bound To ␣-Cd-mentioning

confidence: 99%