Carbohydrate Binding Module Family 5

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• Author: Manjeet Kaur
• Responsible Curator: Appa Rao Podile

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CAZy DB link

https://www.cazy.org/CBM5.html

Ligand specificities

The family 5 carbohydrate binding modules (CBM5) have approximately 60 amino acid residues. The CBM5 are found as accessory domains in chitinases [1, 2, 3, 4], endoglucanases [5] and lytic polysaccharide mono-oxygenases (LPMOs) [6, 7, 8]. This family first originated as a cellulose binding domain family V (CBD V) [1, 9]. However, CBM5 members have now been reported to have affinity to both cellulose and chitin [1, 2, 3, 4, 5, 6, 7, 8, 9]. Deletion of CBM5 from chitinases or LPMOs has shown considerable reduction in chitin binding [4, 6, 8]. The K_d and B_max values for CBM5 of an LPMO from Cellvibrio japonicas, CjLPMO10A for α-chitin, were 5.3 µM and 4.8 µmol/g α-chitin, respectively [6]. The K_d values of CBM5 from Bacillus thuringiensis, BtCBM5 for α- and β-chitin were in the order of 0.6-0.7 µM, whereas the B_max value was ~1.9 µmol/g for both α- and β-chitin [8].

Structural Features

Figure 1. CBM5 of an endoglucanase from Erwinia chrysanthemi PDB ID 1AIW showing surface exposed aromatic residues (Trp18, Trp43 and Tyr44) and a conserved disulfide bond between Cys4 and Cys61.

The structures of CBM5 domains have been elucidated for an endoglucanase, CBDEGZ from Erwinia chrysanthemi (EcEGZCBM5) and two chitinases, ChBDChiB from Serratia marcescens (SmChiBCBM5) and ChBDChiC from Streptomyces griseus HUT6037 (SgChiCCBM5) [1, 2, 5].

The three structures revealed that CBM5s are composed of five β-strands (β1-5) [1, 2, 5]. The β1, β2 and β3 forms the principle structure and the additional short β-strands (β4 and β5) form an antiparallel β-sheet which is independent of the main strand. The EcEGZCBM5 resembles a ski-boot or L-shaped structure composed of only β-sheets [5]. Helix structures have not been found in CBM5 modules.

There are a few differences in CBM5 structures from endo-glucanases (EcEGZCBM5) and chitinases (SmChiBCBM5 and SgChiCCBM5). The EcEGZCBM5 possesses a conserved disulfide bond between Cys4 and Cys61 (Figure 1) [5]. These disulfide bonds have not been reported in SmChiBCBM5 and SgChiCCBM5 [1, 2].

CBM5 modules possess surface exposed aromatic residues which interact with polysaccharides most probably through hydrophobic interactions [1, 9]. These aromatic residues form a flat platform to bind to the planar surfaces of crystalline cellulose/chitin. CBM5 are thus classified under type A CBMs [10]. The EcEGZCBM5 PDB ID 1AIW possesses three exposed aromatic residues: Trp18, Trp43 and Tyr44 (Figure 1). Trp18 is present on an extra loop, is linearly aligned to Trp43 and Tyr44 and extends the substrate binding site [5]. The three residues are essential for complete binding of EcEGZCBM5. Polar residues like Asp17 are present on the cellulose binding face and form H-bonds to stabilize the appropriate orientation of cellulose binding residues [5]. Polar residues also form H-bonds with oxygen atoms and/or OH-groups of glucose subunits of cellulose and thus have been proposed to play a role in cellulose-disruption [5]. Mutation of Asp17 resulted in decreased binding towards cellulose [9].

SmChiBCBM5 and SgChiCCBM5 have only two surface exposed aromatic residues, Trp479 and Trp481 in SmChiBCBM5 and Trp59 and Trp60 in SgChiCCBM5; whose structural homologues in EcEGZCBM5 are Trp43 and Tyr44 [2]. The two exposed aromatic residues are sufficient for binding in SmChiBCBM5 and SgChiCCBM5 [1]. These residues interact extensively and play a vital role in increasing the proximity of substrate through hydrophobic interactions. It has been proposed that either of the two exposed residues should be a tryptophan residue as the Tyr-Tyr pair has not been found in the family [1].

In SgChiCCBM5, six residues (Trp36, Val 48, Tyr 50, Tyr55, Pro66 and Trp72) participate in forming a hydrophobic core in the domain centre. The side chain of Pro66 is internally buried while the remaining 5 residues form the hydrophobic socket [1]. Only two surface exposed aromatic residues (Trp59 and Trp60), which are positioned on a loop between the sheets β2 and β5, are involved in carbohydrate binding [1]. When protein-substrate interactions were studied between SgChiCCBM5 and tri-N-acetyl-chitotriose, it was found that the ligand binding was facilitated by two stacking interactions (Trp59-NAG-1 and Trp-NAG3) and two H-bonds (Trp60-N and NAG2-O7 and Trp56-NE1 and NAG2-O6) [1].

Functionalities

Multi-modular enzymes like endo-glucanases, chitinases and LPMOs possess CBM5 modules as accessory domains appended to their catalytic domain, either directly or with the help of linkers like FnIII domains [1, 2, 3, 4, 5, 6, 7, 8]. The CBM5 domains are responsible for increased affinity of these enzymes towards crystalline cellulose or chitin. Their presence also increases the efficiency of enzymes to bind to substrates in a broader pH range [3, 8]. Deletion of the CBM5 resulted in reduction or complete loss of binding in several instances [4]. Deletion of C-terminal FnIII and CBM5 domains from BliChi resulted in 5-fold reduction of hydrolytic activity on β-chitin and the mutant was unable to degrade α-chitin [4]. Accessory domains have thus been suggested to play an important role in hydrolysis by moving the enzymes in close proximity of substrates [8]. Presence of CBM5 domains in LPMOs have been shown to alter the product profile while acting on crystalline β-chitin substrates [8]. In BcLPMO10A, CBM5 promoted substrate binding as well as protected the enzyme from inactivation [7].

Family Firsts

First indentified

CBM5 modules were first discovered in Endoglucanase, CBDEGZ from Erwinia chrysanthemi (EcEGZCBM5) [5].

First structural characterization

The first NMR derived structure of CBM5 was from EcEGZCBM5 PDB ID 1AIW [5] and first crystal structure was studied for ChBDChiB from Serratia marcescens (SmChiBCBM5) PDB ID 1E15 [2].

References

1. Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T, and Nonaka T. (2006). Structural studies of a two-domain chitinase from Streptomyces griseus HUT6037. J Mol Biol. 2006;358(2):472-84. DOI:10.1016/j.jmb.2006.02.013 |
2. van Aalten DM, Synstad B, Brurberg MB, Hough E, Riise BW, Eijsink VG, and Wierenga RK. (2000). Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-A resolution. Proc Natl Acad Sci U S A. 2000;97(11):5842-7. DOI:10.1073/pnas.97.11.5842 |
3. Uni F, Lee S, Yatsunami R, Fukui T, and Nakamura S. (2012). Mutational analysis of a CBM family 5 chitin-binding domain of an alkaline chitinase from Bacillus sp. J813. Biosci Biotechnol Biochem. 2012;76(3):530-5. DOI:10.1271/bbb.110835 |
4. Manjeet K, Purushotham P, Neeraja C, and Podile AR. (2013). Bacterial chitin binding proteins show differential substrate binding and synergy with chitinases. Microbiol Res. 2013;168(7):461-8. DOI:10.1016/j.micres.2013.01.006 |
5. Brun E, Moriaud F, Gans P, Blackledge MJ, Barras F, and Marion D. (1997). Solution structure of the cellulose-binding domain of the endoglucanase Z secreted by Erwinia chrysanthemi. Biochemistry. 1997;36(51):16074-86. DOI:10.1021/bi9718494 |
6. Forsberg Z, Nelson CE, Dalhus B, Mekasha S, Loose JS, Crouch LI, Røhr ÅK, Gardner JG, Eijsink VG, and Vaaje-Kolstad G. (2016). Structural and Functional Analysis of a Lytic Polysaccharide Monooxygenase Important for Efficient Utilization of Chitin in Cellvibrio japonicus. J Biol Chem. 2016;291(14):7300-12. DOI:10.1074/jbc.M115.700161 |
7. Mutahir Z, Mekasha S, Loose JSM, Abbas F, Vaaje-Kolstad G, Eijsink VGH, and Forsberg Z. (2018). Characterization and synergistic action of a tetra-modular lytic polysaccharide monooxygenase from Bacillus cereus. FEBS Lett. 2018;592(15):2562-2571. DOI:10.1002/1873-3468.13189 |
8. Manjeet K, Madhuprakash J, Mormann M, Moerschbacher BM, and Podile AR. (2019). A carbohydrate binding module-5 is essential for oxidative cleavage of chitin by a multi-modular lytic polysaccharide monooxygenase from Bacillus thuringiensis serovar kurstaki. Int J Biol Macromol. 2019;127:649-656. DOI:10.1016/j.ijbiomac.2019.01.183 |
9. Simpson HD and Barras F. (1999). Functional analysis of the carbohydrate-binding domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli putative chitinase. J Bacteriol. 1999;181(15):4611-6. DOI:10.1128/JB.181.15.4611-4616.1999 |
10. Gilbert HJ, Knox JP, and Boraston AB. (2013). Advances in understanding the molecular basis of plant cell wall polysaccharide recognition by carbohydrate-binding modules. Curr Opin Struct Biol. 2013;23(5):669-77. DOI:10.1016/j.sbi.2013.05.005 |