Carbohydrate Binding Module Family 2

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• Author: ^^^Elizabeth Ficko-Blean^^^
• Responsible Curator: ^^^Elizabeth Ficko-Blean^^^

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CAZy DB link

https://www.cazy.org/CBM2.html

Ligand specificities

The vast majority of family 2 CBMs (CBM2s), ~95%, are bacterial in origin. These protein modules have been shown to bind to crystalline cellulose [1], insoluble chitin [2] or xylan [3]. The xylan-specific CBM2s bind only to the hemicellulose, while some cellulose binding modules also recognize chitin. The CBM2s from some chitinases show a strong preference for crystalline chitin [2]. Cellulose-specific CBM2s were also shown to bind to xyloglucan, albeit with affinities ~1000 lower than for crystalline cellulose [4]. Extremely weak binding to cellulooligosaccharides was detected in cellulose binding CBM2s using NMR [5]. In contrast affinities of xylan binding CBM2s for their polysaccharide or oligosaccharide ligands with a degree of polymerization of six were similar [6]. Some enzymes contain multiple CBM2s that, with respect to xylan, show enhanced affinity through avidity effects [5]. Isothermal titration calorimetry showed that the binding of cellulose and xylan binding of CBM2s to their target ligands was mediated by entropic [7] and enthalpic [5] forces, respectively. These differences in thermodynamic forces driving ligand recognition was proposed to reflect the conformational freedom of cellulose and xylan in free solution and when bound to CBMs. Family 2 is thus highly unusual, containing both type A and type B CBMs. Labelling of type A crystalline cellulose specific CBMs, including CBM2s, which all present three aromatic planar surface residues, showed differences in specificity for pure forms of crystalline cellulose and plant cell walls [8, 9].

Structural Features

CBM2s generally comprise 90 to 100 residues that adopt a canonical β-jelly-roll fold [10]. The two beta-sheets of these CBMs consist of four (face 1) and five (face 2) antiparallel β-strands, respectively. The structure is sometimes stabilized by a disulphide bridge between the N- and C-terminal regions, but not in all cases. In cellulose binding CBM2s, face 1 presents a planar surface that contains three highly conserved aromatic residues (generally tryptophans although tyrosine can also be present) that are positioned to bind to glucose units in linear planar cellulose chains present in the crystalline polysaccharide. The corresponding aromatic residues interact with N-acetylglucosamine residues in chitin [2]. Mutagenesis and chemical modfication studies confirmed the critical role played by the aromatic residues in cellulose recognition [11, 12, 13]. The central tryptophan plays a more important role in ligand binding than the distal aromatic amino acids [12]. In xylan binding CBM2s face 1 displays a slightly concave surface that contains only two tryptophan residues [14]. The perpendicular orientation (with respect to each other) and location of these two tryptophan residues indicate that they interact with xylose residues n and n+2 in the three fold-helical structure of xylan chains. NMR titration experiments with xylooligosaccharides and mutagenesis studies showed that both aromatic residues play a critical role in xylan recognition. An arginine residue adjacent to one of the tryptophans forces it into perpendicular orientation with respect to the other surface aromatic residue. In cellulose binding CBM2s the corresponding perpendicular tryptophan (in xylan binding CBM2s) is planar with the other two surface aromatic residues. The adoption of the planar orientation was predicted to be mediated by the replacement of the arginine (in xylan binding CBM2s) with glycine in cellulose specific CBM2s. It was proposed that this created the required space for the tryptophan to adopt the planar orientation with respect to the other aromatic residues in face 1 [15]. Mutagenesis studies showed that substituting the arginine with glycine in a xylan binding CBM2 abrogated xylan binding but introduced cellulose recognition [14]. Mutagenesis studies showed that alanine substitution of polar residues predicted to interact with CBM2 ligands did not influence affinity for xylan or cellulose, demonstrating that hydrophobic forces dominated carbohydrate recognition [12, 16].

Functionalities

CBM2s that target cellulose as the principle ligand have been reported in cellulases [1], xylan degrading enzymes (xylanases, arabinofuranosidases, esterases) [17, 18] (17,18), pectate lyases [19], mannanases [20] and lytic polysaccharide monooxygenases (LPMOs) [21, 22] (20,21). Xylan and chitin binding CBM2s are restricted to enzymes that target these polysaccharides [2, 3]. Many of these modular enzymes contain CBMs in addition to CBM2 [23], with CBM10-CBM2 modular motifs being particularly common in glycoside hydrolases from Cellvibrio japonicus [24] and Saccharophagus degradans [25]. CBM2s are linked to catalytic modules by linker sequences that are required to be >15 residues in length to maximize the boost in activity provided by the CBM [26, 27]. Cellulases and chitinases substantially potentiate the activity of cellulases and chitinsaes against purified insoluble or crystalline forms of cellulose and chitin, respectively [1, 2]. It has been proposed that cellulase-derived CBM2s enhance enzyme activity by increasing the local concentration or proximity of the enzyme in the vicinity of the substrate [5]. It has, however, also been reported that a CBM2 was able to disrupt the structure of crystalline cellulose leading to enhanced enzyme activity [28]. Cell wall imaging studies have also shown that cellulose and xylan binding CBM2s enhance the activity of a pectate lyase, arabinofuranosidase and xylanases against plant cell walls [29]. Although CBM2s can bind irreversibly to crystalline cellulose [30], fluorescent bleaching experiments showed that these protein modules can migrate across the surface of the polysaccharide [31]. CBM2s have been explored as both affinity tags for purifying proteins and in the immobilization of industrially relevant enzymes to insoluble matrices [30, 32]. These modules are also deployed in the exploration of the architecture of plant cell walls [33].

Family Firsts

CBM2s were first discovered in the cellulase CenA and the xylanase CexA from Cellulomonas fimi. These modules were identified through treatment of these enzymes with proteinases, which resulted in the loss of the C-terminal region comprising the CBM2, which reduced binding to cellulose and, in the case of CenA, activity against crystalline forms of the polysaccharide [1]. In the early literature CBM2s were referred to as cellulose binding domains or CBDs.

The first 3D structure of a CBM2 (binds cellulose), which was determined by NMR, was the C. fimi xylanase Cex [10]. The first structure of a xylan binding CBM, also elucidated by NMR, was from the C. fimi xylanase Xyn11A [14]. The first crystal structure of a CBM2a was that of the chitin binding module from the Pyrococcus chitinase Chi18A [2].

References

1. Gilkes NR, Warren RA, Miller RC Jr, and Kilburn DG. (1988). Precise excision of the cellulose binding domains from two Cellulomonas fimi cellulases by a homologous protease and the effect on catalysis. J Biol Chem. 1988;263(21):10401-7. | Google Books | Open Library
2. Nakamura T, Mine S, Hagihara Y, Ishikawa K, Ikegami T, and Uegaki K. (2008). Tertiary structure and carbohydrate recognition by the chitin-binding domain of a hyperthermophilic chitinase from Pyrococcus furiosus. J Mol Biol. 2008;381(3):670-80. DOI:10.1016/j.jmb.2008.06.006 |
3. Black GW, Hazlewood GP, Millward-Sadler SJ, Laurie JI, and Gilbert HJ. (1995). A modular xylanase containing a novel non-catalytic xylan-specific binding domain. Biochem J. 1995;307 ( Pt 1)(Pt 1):191-5. DOI:10.1042/bj3070191 |
4. Hernandez-Gomez MC, Rydahl MG, Rogowski A, Morland C, Cartmell A, Crouch L, Labourel A, Fontes CM, Willats WG, Gilbert HJ, and Knox JP. (2015). Recognition of xyloglucan by the crystalline cellulose-binding site of a family 3a carbohydrate-binding module. FEBS Lett. 2015;589(18):2297-303. DOI:10.1016/j.febslet.2015.07.009 |
5. Bolam DN, Ciruela A, McQueen-Mason S, Simpson P, Williamson MP, Rixon JE, Boraston A, Hazlewood GP, and Gilbert HJ. (1998). Pseudomonas cellulose-binding domains mediate their effects by increasing enzyme substrate proximity. Biochem J. 1998;331 ( Pt 3)(Pt 3):775-81. DOI:10.1042/bj3310775 |
6. Bolam DN, Xie H, White P, Simpson PJ, Hancock SM, Williamson MP, and Gilbert HJ. (2001). Evidence for synergy between family 2b carbohydrate binding modules in Cellulomonas fimi xylanase 11A. Biochemistry. 2001;40(8):2468-77. DOI:10.1021/bi002564l |
7. Creagh AL, Ong E, Jervis E, Kilburn DG, and Haynes CA. (1996). Binding of the cellulose-binding domain of exoglucanase Cex from Cellulomonas fimi to insoluble microcrystalline cellulose is entropically driven. Proc Natl Acad Sci U S A. 1996;93(22):12229-34. DOI:10.1073/pnas.93.22.12229 |
8. Blake AW, McCartney L, Flint JE, Bolam DN, Boraston AB, Gilbert HJ, and Knox JP. (2006). Understanding the biological rationale for the diversity of cellulose-directed carbohydrate-binding modules in prokaryotic enzymes. J Biol Chem. 2006;281(39):29321-9. DOI:10.1074/jbc.M605903200 |
9. McLean BW, Boraston AB, Brouwer D, Sanaie N, Fyfe CA, Warren RA, Kilburn DG, and Haynes CA. (2002). Carbohydrate-binding modules recognize fine substructures of cellulose. J Biol Chem. 2002;277(52):50245-54. DOI:10.1074/jbc.M204433200 |
10. McLean BW, Boraston AB, Brouwer D, Sanaie N, Fyfe CA, Warren RA, Kilburn DG, and Haynes CA. (2002). Carbohydrate-binding modules recognize fine substructures of cellulose. J Biol Chem. 2002;277(52):50245-54. DOI:10.1074/jbc.M204433200 |
11. Bray MR, Johnson PE, Gilkes NR, McIntosh LP, Kilburn DG, and Warren RA. (1996). Probing the role of tryptophan residues in a cellulose-binding domain by chemical modification. Protein Sci. 1996;5(11):2311-8. DOI:10.1002/pro.5560051117 |
12. McLean BW, Bray MR, Boraston AB, Gilkes NR, Haynes CA, and Kilburn DG. (2000). Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues. Protein Eng. 2000;13(11):801-9. DOI:10.1093/protein/13.11.801 |
13. Nagy T, Simpson P, Williamson MP, Hazlewood GP, Gilbert HJ, and Orosz L. (1998). All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands. FEBS Lett. 1998;429(3):312-6. DOI:10.1016/s0014-5793(98)00625-5 |
14. Simpson PJ, Bolam DN, Cooper A, Ciruela A, Hazlewood GP, Gilbert HJ, and Williamson MP. (1999). A family IIb xylan-binding domain has a similar secondary structure to a homologous family IIa cellulose-binding domain but different ligand specificity. Structure. 1999;7(7):853-64. DOI:10.1016/s0969-2126(99)80108-7 |
34. Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
35. Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
36. Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
37. Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |