CBM3d, a novel subfamily of family 3 carbohydrate-binding modules identified in Cel48A exoglucanase of Cellulosilyticum ruminicola

Journal of Bacteriology

Volumn 193, Issue 19, 2011, Pages 5199-5206

  Cai, Shichun ^a   Zheng, Xin ^a   Dong, Xiuzhu ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOHYDRATE BINDING PROTEIN; CBM3D PROTEIN; CEL48A EXOGLUCANASE; CHITIN; GLUCAN GLUCOSIDASE; MICROCRYSTALLINE CELLULOSE; UNCLASSIFIED DRUG;

ARTICLE; CELLULOSILYTICUM RUMINICOLA; ENZYME ACTIVITY; ENZYME SPECIFICITY; GENE EXPRESSION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN PURIFICATION; PROTEIN SECONDARY STRUCTURE; RUMEN MICROORGANISM; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; GRAM-POSITIVE BACTERIA; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; PHYLOGENY; POLYSACCHARIDES, BACTERIAL; PROTEIN BINDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 80053588283     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05227-11     Document Type: Article

References (31)

1. Boraston, A. B., D. N. Bolam, H. J. Gilbert, and G. J. Davies. 2004. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem. J. 382:769-781.
2. Boraston, A., et al. 1998. The structure and function of cellulose binding domains, p. 139-146. In M. Claeyssen, W. Nerinkx, and K. Piens (ed.), Carbohydrate from Trichoderma reesei and other microorganisms. Royal Society of Chemistry, Cambridge, United Kingdom.
3. Boraston, A. B., et al. 1999. Carbohydrate-binding modules: diversity of structure and function, p. 202-211. In H. J. Gilbert, G. J. Davies, B. Henrissat, and B. Svensson (ed.), Recent advances in carbohydrate bioengineering. Royal Society of Chemistry, Cambridge, United Kingdom.
4. Boraston, A. B., P. Tomme, E. A. Amandoron, and D. G. Kilburn. 2000. A novel mechanism of xylan binding by a lectin-like module from Streptomyces lividans xylanase 10A. Biochem. J. 350:933-941.
5. Cai, S., et al. 2010. Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate-borne fibrolytic enzymes. Appl. Environ. Microbiol. 76:3818-3824.
6. Cantarel, B. L., et al. 2009. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res. 37:D233-D238.
7. Chou, W. I., T. W. Pai, S. H. Liu, B. K. Hsiung, and M. D. Chang. 2006. The family 21 carbohydrate-binding module of glucoamylase from Rhizopus oryzae consists of two sites playing distinct roles in ligand binding. Biochem. J. 396:469-477.
8. Coutinho, J. B., N. R. Gilkes, D. G. Kilburn, R. A. J. Warren, and R. C. Miller, Jr. 1993. The nature of the cellulose-binding domain effects the activities of a bacterial endoglucanase on different forms of cellulose. FEMS Microbiol. Lett. 113:211-217.
9. Din, N., et al. 1994. The cellulose-binding domain of endoglucanase A (CenA) from Cellulomonas fimi: evidence for the involvement of tryptophan residues in binding. Mol. Microbiol. 11:747-755.
10. Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
11. Guillén, D., S. Sánchez, and R. Rodríguez-Sanoja. 2010. Carbohydratebinding domains: multiplicity of biological roles. Appl. Microbiol. Biotechnol. 85:1241-1249.
12. Hall, J., et al. 1995. The non-catalytic cellulose-binding domain of a novel cellulase from Pseudomonas fluorescens subsp. cellulosa is important for the efficient hydrolysis of Avicel. Biochem. J. 309:749-756.
13. Henshaw, J. L., et al. 2004. The family 6 carbohydrate binding module CmCBM6-2 contains two ligand-binding sites with distinct specificities. J. Biol. Chem. 279:21552-21559.
14. Ho, S. N., H. D. Hunt, R. M. Horton, J. K. Pullen, and L. R. Pease. 1989. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59.
15. Hong, J., Y. Wang, X. Ye, and Y. H. P. Zhang. 2008. Simple protein purification through affinity adsorption on regenerated amorphous cellulose followed by intein self-cleavage. J. Chromatogr. A 1194:150-154.
16. Jindou, S., et al. 2006. Novel architecture of family-9 glycoside hydrolases identified in cellulosomal enzymes of Acetivibrio cellulolyticus and Clostridium thermocellum. FEMS Microbiol. Lett. 254:308-316.
17. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
18. Li, Y., D. C. Irwin, and D. B. Wilson. 2007. Processivity, substrate binding, and mechanism of cellulose hydrolysis by Thermobifida fusca Cel9A. Appl. Environ. Microbiol. 73:3165-3172.
19. Limón, M. C., E. Margolles-Clark, T. Benitez, and M. Penttila. 2001. Addition of substrate-binding domains increases substrate-binding capacity and specific activity of a chitinase from Trichoderma harzianum. FEMS Microbiol. Lett. 198:57-63.
20. Lynd, L. R., P. J. Weimer, W. H. Van Zyl, and I. S. Pretorius. 2002. Microbial cellulose utilization: fundamentals and biotechnology. Microbiol. Mol. Biol. Rev. 66:506-577.
21. McLean, B. W., et al. 2000. Analysis of binding of the family 2a carbohydratebinding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues. Protein Eng. Des. Sel. 13:801-809.
22. Michaelis, L., and M. L. Menten. 1913. Die Kinetik den Invert-inwirkung. Biochem. Z. 49:333-369.
23. Miller, G. L. 1959. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31:426-428.
24. Murashima, K., A. Kosugi, and R. H. Doi. 2005. Site-directed mutagenesis and expression of the soluble form of the family IIIa cellulose binding domain from the cellulosomal scaffolding protein of Clostridium cellulovorans. J. Bacteriol. 187:7146-7149.
25. Notenboom, V., A. B. Boraston, S. J. Williams, D. G. Kilburn, and D. R. Roses. 2002. High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding. Biochemistry 41:4246-4254.
26. Petkun, S., et al. 2010. Structure of a family 3b' carbohydrate-binding module from the Cel9V glycoside hydrolase from Clostridium thermocellum: structural diversity and implications for carbohydrate binding. Acta Crystallogr. D Biol. Crystallogr. D66:33-43.
27. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
28. Shimon, L. J., et al. 2000. Structure of a family IIIa scaffoldin CBD from the cellulosome of Clostridium cellulolyticum at 2.2 Å resolution. Acta Crystallogr. Sect. D 56:1560-1568.
29. Sunna, A., M. D. Gibbs, and P. L. Bergquist. 2001. Identification of novel β-mannan- and β-glucan-binding modules: evidence for a superfamily of carbohydrate-binding modules. Biochem. J. 356:791-798.
30. Tormo, J., et al. 1996. Crystal structure of a bacterial family-III cellulosebinding domain: a general mechanism for attachment to cellulose. EMBO J. 15:5739-5751.
31. Yaniv, O., L. J. W. Shimon, E. A. Bayer, R. Lamed, and F. Frolow. 2011. Scaffoldin-borne family 3b carbohydrate-binding module from the cellulosome of Bacteroides cellulosolvens: structural diversity and significance of calcium for carbohydrate binding. Acta Crystallogr. D Biol. Crystal. D67: 506-515.