Small angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum

References

• Abbott, D. W., Ficko-Blean, E., van Bueren, A. L., Rogowski, A., Cartmell, A., Coutinho, P. M., … Boraston, A. B. (2009). Analysis of the structural and functional diversity of plant cell wall specific family 6 carbohydrate binding modules. Biochemistry, 48(43), 10395–10404. doi:10.1021/bi9013424
   PubMed Web of Science ®Google Scholar
• Ahmed, S., Gautam, S., Gupta, M. N., & Goyal, A. (2013d). Analysis of structural element of family 6 carbohydrate-binding module (CtCBM6B) of alpha-L-arabinofuranosidase from Clostridium thermocellum. Journal of Proteins & Proteomics, 4(1). https://jpp.org.in/index.php/jpp/article/view/5.
   Google Scholar
• Ahmed, S., Luis, A. S., Brás, J. L., Fontes, C. M., & Goyal, A. (2013). The family 6 carbohydrate-binding module (CtCBM6B) of Clostridium thermocellum alpha-L-arabinofuranosidase binds xylans and thermally stabilized by Ca2+ ions. Biocatalysis and Biotransformation, 31(4), 217–225. doi:10.3109/10242422.2013.828047
   Web of Science ®Google Scholar
• Ahmed, S., Luís, A. S., Brás, J. L. A., Fontes, C. M. G. A., & Goyal, A. (2013). Functional and structural characterization of family 6 carbohydrate-binding module (CtCBM6A) of Clostridium thermocellum α-L-arabinofuranosidase. Biochemistry (Moscow), 78(11), 1272–1279. doi:10.1134/S0006297913110072
   PubMed Web of Science ®Google Scholar
• Ahmed, S., Luis, A. S., Bras, J. L., Ghosh, A., Gautam, S., Gupta, M. N., … Goyal, A. (2013). A novel α-l-arabinofuranosidase of family 43 glycoside hydrolase (Ct43Araf) from Clostridium thermocellum. PloS One, 8(9), e73575. doi:10.1371/journal.pone.0073575
   PubMed Web of Science ®Google Scholar
• Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215 (3), 403–410.. doi:10.1016/S0022-2836(05)80360-2
   PubMed Web of Science ®Google Scholar
• Beldman, G., Schols, H. A., Pitson, S. M., Searle-van Leeuwen, M. J. F., & Voragen, A. G. J. (2012). Arabinans and arabinan degrading enzymes. Advances in Macromolecular Carbohydrate Research, 10.1016/s1874-5261(97)80003-0.
   Google Scholar
• Boraston, A. B., McLean, B. W., Chen, G., Li, A., Warren, R. A. J., & Kilburn, D. G. (2002). Co-operative binding of triplicate carbohydrate-binding modules from a thermophilic xylanase. Molecular Microbiology, 43 (1), 187–194. doi:10.1046/j.1365-2958.2002.02730.x
   PubMed Web of Science ®Google Scholar
• Boraston, A. B., Notenboom, V., Warren, R. A. J., Kilburn, D. G., Rose, D. R., & Davies, G. (2003). Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and “galactose-binding” domains. Journal of Molecular Biology, 327 (3), 659–669.. doi:10.1016/S0022-2836(03)00152-9
   PubMed Web of Science ®Google Scholar
• Contesini, F. J., Liberato, M. V., Rubio, M. V., Calzado, F., Zubieta, M. P., Riaño-Pachón, D. M., … Damasio, A. R. (2017). Structural and functional characterization of a highly secreted α-L-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. Biochimica et Biophysica Acta (Bba) - Proteins and Proteomics, 1865 (12), 1758–1769. doi:10.1016/j.bbapap.2017.09.001
   PubMed Web of Science ®Google Scholar
• Czjzek, M., Bolam, D. N., Mosbah, A., Allouch, J., Fontes, C. M., Ferreira, L. M., … Black, G. W. (2001). The location of the ligand-binding site of carbohydrate-binding modules that have evolved from a common sequence is not conserved. Journal of Biological Chemistry, 276 (51), 48580–48587. doi:10.1074/jbc.M109142200
   PubMed Web of Science ®Google Scholar
• Farro, E. G. S., Leite, A. E. T., Silva, I. A., Filgueiras, J. G., de Azevedo, E. R., Polikarpov, I., & Nascimento, A. S. (2018). GH43 endo-arabinanase from Bacillus licheniformis: Structure, activity and unexpected synergistic effect on cellulose enzymatic hydrolysis. International Journal of Biological Macromolecules, 117, 7–16.. doi:10.1016/j.ijbiomac.2018.05.157
   PubMed Web of Science ®Google Scholar
• Fischer, H., de Oliveira Neto, M., Napolitano, H. B., Polikarpov, I., & Craievich, A. F. (2010). Determination of the molecular weight of proteins in solution from a single small-angle X-ray scattering measurement on a relative scale. Journal of Applied Crystallography, 43 (1), 101–109.. doi:10.1107/S0021889809043076
   Google Scholar
• Fontes, C. M. G. A., & Gilbert, H. J. (2010). Cellulosomes: Highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydrates. Annual Review of Biochemistry, 79 (1), 655–681. doi:10.1146/annurev-biochem-091208-085603
   PubMed Web of Science ®Google Scholar
• Franke, D., Petoukhov, M. V., Konarev, P. V., Panjkovich, A., Tuukkanen, A., Mertens, H. D. T., … Svergun, D. I. (2017). ATSAS 2.8: A comprehensive data analysis suite for small-angle scattering from macromolecular solutions. Journal of Applied Crystallography, 50 (4), 1212–1225. doi:10.1107/S1600576717007786
   PubMed Web of Science ®Google Scholar
• Goyal, A., Ahmed, S., Sharma, K., Gupta, V., Bule, P., Alves, V. D., … Najmudin, S. (2016). Molecular determinants of substrate specificity revealed by the structure of Clostridium thermocellum arabinofuranosidase 43A from glycosyl hydrolase family 43 subfamily 16. Acta Crystallographica Section D Structural Biology, 72 (12), 1281–1289. doi:10.1107/S205979831601737X
   PubMedGoogle Scholar
• Harris, D., & DeBolt, S. (2010). Synthesis, regulation and utilization of lignocellulosic biomass. Plant Biotechnology Journal, 8 (3), 244–262. doi:10.1111/j.1467-7652.2009.00481.x
   PubMed Web of Science ®Google Scholar
• Hemsworth, G. R., Thompson, A. J., Stepper, J., Sobala, ŁF., Coyle, T., Larsbrink, J., … Davies, G. J. (2016). Structural dissection of a complex Bacteroides ovatus gene locus conferring xyloglucan metabolism in the human gut. Open Biology, 6(7), 160142. doi:10.1098/rsob.160142
   PubMed Web of Science ®Google Scholar
• Jiménez-García, B., Pons, C., Svergun, D. I., Bernadó, P., & Fernández-Recio, J. (2015). PyDockSAXS: Protein-protein complex structure by SAXS and computational docking. Nucleic Acids Research, 43(W1), W356–W361. doi:10.1093/nar/gkv368
   PubMed Web of Science ®Google Scholar
• Kozin, M. B., & Svergun, D. I. (2001). Automated matching of high- and low-resolution structural models. Journal of Applied Crystallography, 34 (1), 33–41. doi:10.1107/S0021889800014126
   Google Scholar
• Krissinel, E., & Henrick, K. (2004). Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallographica Section D Biological Crystallography, 60 (12), 2256–2268. doi:10.1107/S0907444904026460
   PubMedGoogle Scholar
• Lagaert, S., Pollet, A., Courtin, C. M., & Volckaert, G. (2014). β-Xylosidases and α-L-arabinofuranosidases: Accessory enzymes for arabinoxylan degradation. Biotechnology Advances, 32 (2), 316–332. doi:10.1016/j.biotechadv.2013.11.005
   PubMed Web of Science ®Google Scholar
• Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011). SignalP 4.0: Discriminating signal peptides from transmembrane regions. Nature Methods, 8 (10), 785–786. doi:10.1038/nmeth.1701
   PubMed Web of Science ®Google Scholar
• Saha, B. C. (2000). α-L-Arabinofuranosidases: Biochemistry, molecular biology and application in biotechnology. Biotechnology Advances, 18 (5), 403–423. doi:10.1016/S0734-9750(00)00044-6
   PubMed Web of Science ®Google Scholar
• Saleh, M. A., Han, W.-J., Lu, M., Wang, B., Li, H., Kelly, R. M., & Li, F.-L. (2017). Two distinct α-l-Arabinofuranosidases in Caldicellulosiruptor species drive degradation of arabinose-based polysaccharides. Applied and Environmental Microbiology, 83 (13), e00574–17. doi:10.1128/AEM.00574-17
   PubMed Web of Science ®Google Scholar
• Sharma, K., Fontes, C. M. G. A., Najmudin, S., & Goyal, A. (2019). Molecular organization and protein stability of the Clostridium thermocellum glucuronoxylan endo-β-1,4-xylanase of family 30 glycoside hydrolase in solution. Journal of Structural Biology, 206 (3), 335–344.. doi:10.1016/j.jsb.2019.04.005
   PubMed Web of Science ®Google Scholar
• Shoseyov, O., Shani, Z., & Levy, I. (2006). Carbohydrate Binding Modules: Biochemical Properties and Novel Applications. Microbiology and Molecular Biology Reviews, 70 (2), 283–295. doi:10.1128/MMBR.00028-05
   PubMed Web of Science ®Google Scholar
• Svergun, D. I. (1992). Determination of the regularization parameter in indirect-transform methods using perceptual criteria. Journal of Applied Crystallography, 25 (4), 495–503. doi:10.1107/S0021889892001663
   Web of Science ®Google Scholar
• Svergun, D. I. (1999). Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophysical Journal, 76 (6), 2879–2886. doi:10.1016/S0006-3495(99)77443-6
   PubMed Web of Science ®Google Scholar
• Svergun, D. I., Petoukhov, M. V., & Koch, M. H. J. (2001). Determination of domain structure of proteins from x-ray solution scattering. Biophysical Journal, 80 (6), 2946–2953. doi:10.1016/S0006-3495(01)76260-1
   PubMed Web of Science ®Google Scholar
• Thakur, A., Sharma, K., & Goyal, A. (2019). α-l-Arabinofuranosidase: A Potential Enzyme for the Food Industry. In Green Bio-processes. (pp. 229–244). Singapore: Springer.
   Google Scholar
• Touw, W. G., Baakman, C., Black, J., Te Beek, T. A. H., Krieger, E., Joosten, R. P., & Vriend, G. (2015). A series of PDB-related databanks for everyday needs. Nucleic Acids Research, 43(D1), D364–D368. doi:10.1093/nar/gku1028
   PubMed Web of Science ®Google Scholar
• Vandermarliere, E., Bourgois, T. M., Winn, M. D., Van Campenhout, S., Volckaert, G., Delcour, J. A., … Courtin, C. M. (2009). Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family. Biochemical Journal, 418 (1), 39–47. doi:10.1042/BJ20081256
   PubMedGoogle Scholar
• Volkov, V. V., & Svergun, D. I. (2003). Uniqueness of ab initio shape determination in small-angle scattering. Journal of Applied Crystallography, 36 (3), 860–864. doi:10.1107/S0021889803000268
   Google Scholar
• Webb, B., & Sali, A. (2016). Comparative protein structure modeling using MODELLER. Current Protocols in Bioinformatics, 54 (1). doi:10.1002/cpbi.3
   PubMedGoogle Scholar
• Zdobnov, E. M., & Apweiler, R. (2001). InterProScan - An integration platform for the signature-recognition methods in InterPro. Bioinformatics, 17(9), 847–848. doi:10.1093/bioinformatics/17.9.847
   PubMed Web of Science ®Google Scholar
• Zhong, R., Teng, Q., Lee, C., & Ye, Z. H. (2014). Identification of a disaccharide side chain 2-O-α-D-galactopyranosyl-α-D-glucuronic acid in arabidopsis xylan. Plant Signaling and Behavior, 9, 2–6. doi:10.4161/psb.27933.
   Google Scholar