Carbohydrate Binding Module Family 2

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

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CAZy DB link

http://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 ~1000x 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 CBM2 interactions with their target cellulose or xylan ligands were 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 cellulose binding type A and xylan binding 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

Figure 1. The fold of the CBM2 in the Cellulomonas fimi GH10 xylanase Xyn10A (also known as Cex)(see PDB ID 1exg) highlighting the three planar tryptophans that are optimised to bind to the planar surface of crystalline cellulose bound.

Figure 2. The fold of the CBM2 in the Cellulomonas fimi GH11 xylanase Xyn11D (PDB ID 2xbd) highlighting the two perpendicular tryptophans that are optimised to bind to xylose units n and n+2 in the three-fold helical structure of xylan. The tryptophan perpendicular to the surface of the CBM is mediated through a stacking interaction with a surface arginine, which is also shown.

CBM2s generally comprise 90 to 100 residues that adopt a canonical β-jelly-roll fold (see PDB ID 1exg for an example) [10]. The two β-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 (Figure 1). 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 (see PDB ID 2xbd for an example) face 1 displays a slightly concave surface that contains only two tryptophan residues [14]. The perpendicular orientation (with respect to each other; Figure 2) 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 (Figure 2). In cellulose binding CBM2s the corresponding perpendicular tryptophan (in xylan binding CBM2s) is planar with the other two surface aromatic residues (see PDB ID 1e5b). 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 created a planar orientation for both surface tryptophans (see Fig. 5 and 6 in [15]), abrogated xylan binding and introduced cellulose recognition [15]. 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], pectate lyases [19], mannanases [20] and lytic polysaccharide monooxygenases (LPMOs) [21, 22]. Xylan and chitin binding CBM2s are restricted to enzymes that target these polysaccharides [2, 3]. Many of these modular enzymes contain other CBM families 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]. CBM2s 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

First Identified:

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.

First structural characterization:

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

References

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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 |
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 |
17. Kellett LE, Poole DM, Ferreira LM, Durrant AJ, Hazlewood GP, and Gilbert HJ. (1990). Xylanase B and an arabinofuranosidase from Pseudomonas fluorescens subsp. cellulosa contain identical cellulose-binding domains and are encoded by adjacent genes. Biochem J. 1990;272(2):369-76. DOI:10.1042/bj2720369 |
18. Ferreira LM, Wood TM, Williamson G, Faulds C, Hazlewood GP, Black GW, and Gilbert HJ. (1993). A modular esterase from Pseudomonas fluorescens subsp. cellulosa contains a non-catalytic cellulose-binding domain. Biochem J. 1993;294 ( Pt 2)(Pt 2):349-55. DOI:10.1042/bj2940349 |
21. Crouch LI, Labourel A, Walton PH, Davies GJ, and Gilbert HJ. (2016). The Contribution of Non-catalytic Carbohydrate Binding Modules to the Activity of Lytic Polysaccharide Monooxygenases. J Biol Chem. 2016;291(14):7439-49. DOI:10.1074/jbc.M115.702365 |
22. Forsberg Z, Mackenzie AK, Sørlie M, Røhr ÅK, Helland R, Arvai AS, Vaaje-Kolstad G, and Eijsink VG. (2014). Structural and functional characterization of a conserved pair of bacterial cellulose-oxidizing lytic polysaccharide monooxygenases. Proc Natl Acad Sci U S A. 2014;111(23):8446-51. DOI:10.1073/pnas.1402771111 |
23. Bolam DN, Xie H, Pell G, Hogg D, Galbraith G, Henrissat B, and Gilbert HJ. (2004). X4 modules represent a new family of carbohydrate-binding modules that display novel properties. J Biol Chem. 2004;279(22):22953-63. DOI:10.1074/jbc.M313317200 |
26. Ferreira LM, Durrant AJ, Hall J, Hazlewood GP, and Gilbert HJ. (1990). Spatial separation of protein domains is not necessary for catalytic activity or substrate binding in a xylanase. Biochem J. 1990;269(1):261-4. DOI:10.1042/bj2690261 |
29. Hervé C, Rogowski A, Blake AW, Marcus SE, Gilbert HJ, and Knox JP. (2010). Carbohydrate-binding modules promote the enzymatic deconstruction of intact plant cell walls by targeting and proximity effects. Proc Natl Acad Sci U S A. 2010;107(34):15293-8. DOI:10.1073/pnas.1005732107 |
31. Jervis EJ, Haynes CA, and Kilburn DG. (1997). Surface diffusion of cellulases and their isolated binding domains on cellulose. J Biol Chem. 1997;272(38):24016-23. DOI:10.1074/jbc.272.38.24016 |
33. McCartney L, Blake AW, Flint J, Bolam DN, Boraston AB, Gilbert HJ, and Knox JP. (2006). Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modules. Proc Natl Acad Sci U S A. 2006;103(12):4765-70. DOI:10.1073/pnas.0508887103 |