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Carbohydrate Binding Module Family 21
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- Authors: ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
- Responsible Curators: ^^^Birte Svensson^^^ and ^^^Stefan Janecek^^^
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Modules from family CBM21 bind to the α-glucan starch and oligosaccharides derived from starch or related to such oligosaccharides that contain α-1,4-linked glucose and/or α-1,6-linked glucose including maltose through maltoheptaose, β- and γ-cyclodextrins, isomaltotriose and isomaltotetraose [1, 2, 3, 4]. CBM21 also interacts with amylose and alters its ultrastructure as demonstrated by atomic force microscopy . Circular permutation enhanced the affinity for amylose . The domain has been described as providing mainly glucoamylase and α-amylase with the ability to bind onto raw-starch (starch granules) [7, 8, 9, 10, 11].
Structures of CBM21 have been determined by NMR and X-ray crystallography both in free and in carbohydrate complexed form. They adopt a common β-sandwich fold and have two binding sites accommodating carbohydrate ligands similarly to other starch binding domains. The binding sites contain aromatic side chains participating in carbohydrate interaction. Initially it was described by modelling using an NMR structure of a CBM20 as template  and thereafter by docking onto the NMR structure determined for CBM21 from the family GH15 Rhizopus oryzae glucoamylase . The crystal structure determined for this CBM21 in complex with β-cyclodextrin or maltoheptaose identified W47, Y83 and Y94 interacting at site I and Y32 and F58 at site II for both ligands . Site I requires ligands with DP > 3 for binding . A CBM21-like domain was identified in the crystal structure of barley family GH13 limit dextrinase .
CBM21s are mainly associated with some fungal glucoamylases and α-amylases of the family GH15 [7, 8, 9] and GH13 [10, 11], respectively. This was confirmed by an exhaustive evolutionary analysis of 85 fungal genomes . In both cases, i.e. in GH15 glucoamylases and GH13 α-amylases, the CBM21 precedes the catalytic domain . The CBM21 is present also as a part of the regulatory subunit of Ser/Thr-specific protein phosphatases that directs the protein phosphatase to glycogen . Recently, a structural comparison identified an N-terminal CBM21-like domain in the barley GH13 limit dextrinase , where it is followed by the module from the family CBM48 succeeded by the catalytic TIM-barrel.
- First Identified
Family CBM21 was first observed as an N-terminally located domain in glucoamylase from Rhizopus oryzae . The function was ascribed based on comparison of multiple forms of the glucoamylase [7, 16] and amino acid sequence alignment . The CBM21 sequence was revealed as related to that of the starch binding domain of Aspergillus niger glucoamylase , which has been assigned the family CBM20 [14, 19, 20].
- First Structural Characterization
The first CBM21 three-dimensional structure was determined by NMR for the module from the family GH15 glucoamylase from Rhizopus oryzae . The first CBM21 complex structures were determined by X-ray crystallography for that domain binding to β-cyclodextrin or maltoheptaose .
The CBM21 from Rhizopus oryzae glucoamylase has been introduced as a novel affinity purification tag .
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- Chu CH, Li KM, Lin SW, Chang MD, Jiang TY, and Sun YJ. (2014). Crystal structures of starch binding domain from Rhizopus oryzae glucoamylase in complex with isomaltooligosaccharide: insights into polysaccharide binding mechanism of CBM21 family. Proteins. 2014;82(6):1079-85. DOI:10.1002/prot.24446 |
- Liu YN, Lai YT, Chou WI, Chang MD, and Lyu PC. (2007). Solution structure of family 21 carbohydrate-binding module from Rhizopus oryzae glucoamylase. Biochem J. 2007;403(1):21-30. DOI:10.1042/BJ20061312 |
- Tung JY, Chang MD, Chou WI, Liu YY, Yeh YH, Chang FY, Lin SC, Qiu ZL, and Sun YJ. (2008). Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path. Biochem J. 2008;416(1):27-36. DOI:10.1042/BJ20080580 |
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- Stephen P, Cheng KC, and Lyu PC. (2012). Crystal structure of circular permuted RoCBM21 (CP90): dimerisation and proximity of binding sites. PLoS One. 2012;7(11):e50488. DOI:10.1371/journal.pone.0050488 |
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- Chen W, Xie T, Shao Y, and Chen F. (2012). Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi. PLoS One. 2012;7(11):e49679. DOI:10.1371/journal.pone.0049679 |
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Tanaka Y, Ashikari T, Nakamura N, Kiuchi N, Shibano Y, Amachi T, and Yoshizumi H. Comparison of amino acid sequences of three glucoamylases and their structure-function relationships. Agric. Biol. Chem. 1986; 50: 965-9.
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- Christiansen C, Abou Hachem M, Janecek S, Viksø-Nielsen A, Blennow A, and Svensson B. (2009). The carbohydrate-binding module family 20--diversity, structure, and function. FEBS J. 2009;276(18):5006-29. DOI:10.1111/j.1742-4658.2009.07221.x |
- Lin SC, Lin IP, Chou WI, Hsieh CA, Liu SH, Huang RY, Sheu CC, and Chang MD. (2009). CBM21 starch-binding domain: a new purification tag for recombinant protein engineering. Protein Expr Purif. 2009;65(2):261-6. DOI:10.1016/j.pep.2009.01.008 |