PS51173

CBM2 (Carbohydrate-binding type-2) domain profile

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Short nameCBM2

Description

The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (EC 3.2.1.4), cellobiohydrolases (EC 3.2.1.91) (exoglucanases), or xylanases (EC 3.2.1.8)
[5]
. Structurally, cellulases and xylanases generally consist of a catalytic domain and a conserved region of ~100 amino acid residues, the carbohydrate-binding module 2 (CBM2)
[3]
. It is found either at the N-terminal or at the C-terminal extremity of these enzymes. CBM2 can be classified in 2 subfamilies according to substrate specificities: CBM2a which binds cellulose and CBM2b which interacts specifically with xylan. CBM2a and CBM2b also display significant differences at the residue level as shown in the following schematic representation: +-------------------------------------------------+ | | CBM2a xCxxxxWxxGxxNxxxxxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx ******** +-------------------------------------------------+ | | CBM2b xCxxxxWxxRxxNxxxxxxxxxxxWxxxxxxx--------GxxxxxxxxxxCx 'C': conserved cysteine involved in a disulfide bond. '*': position of the pattern. 'W': surface-exposed tryptophan Like other CBM domains CBM2 is a beta-sheet domain containing a planar face which interacts with its ligand via a hydrophobic strip of aromatic residues
[4]
. In family 2a this hydrophobic surface consists of three tryptophan residues, which are all required for binding soluble and insoluble forms of cellulose
[2]
. In family 2b only 2 surface-exposed tryptophans are conserved and the first one is oriented differently. It is therefore not well oriented to interact with cellulose but is ideal for binding xylan
[1]
. Enzymes known to contain such a domain are: - Endoglucanase (gene end1) from Butyrivibrio fibrisolvens. - Endoglucanases A (gene cenA) and B (cenB) from Cellulomonas fimi. - Exoglucanases A (gene cbhA) and B (cbhB) from Cellulomonas fimi. - Endoglucanase E-2 (gene celB) from Thermomonospora fusca. - Endoglucanase A (gene celA) from Microbispora bispora. - Endoglucanases A (gene celA), B (celB) and C (celC) from Pseudomonas fluorescens. - Endoglucanase A (gene celA) from Streptomyces lividans. - Exocellobiohydrolase (gene cex) from Cellulomonas fimi. - Xylanases A (gene xynA) and B (xynB) from Pseudomonas fluorescens. - Arabinofuranosidase C (EC 3.2.1.55) (xylanase C) (gene xynC) from Pseudomonas fluorescens. - Chitinase 63 (EC 3.2.1.14) from Streptomyces plicatus. - Chitinase C from Streptomyces lividans. To recognize the CBM2a domain we developed a pattern which is located in a conserved region specific to CBM2a. We also developed a profile which covers the whole CBM2 domain and recognizes both CBM2 subfamilies.

References

1.A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity. Simpson PJ, Bolam DN, Cooper A, Ciruela A, Hazlewood GP, Gilbert HJ, Williamson MP. Structure 7, 853-64, (1999). View articlePMID: 10425686

2.All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands. Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, Orosz L. FEBS Lett. 429, 312-6, (1998). View articlePMID: 9662439

3.Bacterial cellulose-binding domain-like sequences in eucaryotic polypeptides. Meinke A, Gilkes NR, Kilburn DG, Miller RC Jr, Warren RA. Protein Seq. Data Anal. 4, 349-53, (1991). PMID: 1812490

4.Solution structure of a cellulose-binding domain from Cellulomonas fimi by nuclear magnetic resonance spectroscopy. Xu GY, Ong E, Gilkes NR, Kilburn DG, Muhandiram DR, Harris-Brandts M, Carver JP, Kay LE, Harvey TS. Biochemistry 34, 6993-7009, (1995). View articlePMID: 7766609

5.Domains in microbial beta-1, 4-glycanases: sequence conservation, function, and enzyme families. Gilkes NR, Henrissat B, Kilburn DG, Miller RC Jr, Warren RA. Microbiol. Rev. 55, 303-15, (1991). View articlePMID: 1886523

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