Browse > Article
http://dx.doi.org/10.4014/jmb.1208.08043

Structural Analysis of ${\alpha}$-L-Arabinofuranosidase from Thermotoga maritima Reveals Characteristics for Thermostability and Substrate Specificity  

Dumbrepatil, Arti (Department of Food Science and Technology, Chungbuk National University)
Park, Jung-Mi (Department of Food Science and Technology, Chungbuk National University)
Jung, Tae Yang (Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology)
Song, Hyung-Nam (Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology)
Jang, Myoung-Uoon (Department of Food Science and Technology, Chungbuk National University)
Han, Nam Soo (Department of Food Science and Technology, Chungbuk National University)
Kim, Tae-Jip (Department of Food Science and Technology, Chungbuk National University)
Woo, Eui Jeon (Medical Proteomics Research Center, Korea Research Institute of Biosciences and Biotechnology)
Publication Information
Journal of Microbiology and Biotechnology / v.22, no.12, 2012 , pp. 1724-1730 More about this Journal
Abstract
An ${\alpha}$-L-arabinofuranosidase (TmAFase) from Thermotoga maritima MSB8 is a highly thermostable exo-acting hemicellulase that exhibits a relatively higher activity towards arabinan and arabinoxylan, compared with other glycoside hydrolase 51 family enzymes. In the present study, we carried out the enzymatic characterization and structural analysis of TmAFase. Tight domain associations found in TmAFase, such as an inter-domain disulfide bond (Cys306 and Cys476) in each monomer, a novel extended arm (amino acids 374-385) at the dimer interface, and total 12 salt bridges in the hexamer, may account for the thermostability of the enzyme. One of the xylan binding determinants (Trp96) was identified in the active site, and a region of amino acids (374-385) protrudes out forming an obvious wall at the substrate-binding groove to generate a cavity. The altered cavity shape with a strong negative electrostatic distribution is likely related to the unique substrate preference of TmAFase towards branched polymeric substrates.
Keywords
Thermotoga maritima; ${\alpha}$-L-arabinofuranosidase; structural analysis; X-ray crystallography;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Rémond, C., R. Plantier-Royon, N. Aubry, E. Maes, C. Bliard, and M. J. O'Donohue. 2004. Synthesis of pentose-containing disaccharides using a thermostable alpha-L-arabinofuranosidase. Carbohydr. Res. 339: 2019-2025.   DOI   ScienceOn
2 Saha, B. C. 2000. Alpha-L-arabinofuranosidases: Biochemistry, molecular biology and application in biotechnology. Biotechnol. Adv. 18: 403-423.   DOI   ScienceOn
3 Shallom, D., V. Belakhov, D. Solomon, S. Gilead-Gropper, T. Baasov, G. Shoham, and Y. Shoham. 2002. The identification of the acid-base catalyst of alpha-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycoside hydrolase. FEBS Lett. 514: 163-167.   DOI   ScienceOn
4 Shallom, D. and Y. Shoham. 2003. Microbial hemicellulases. Curr. Opin. Microbiol. 6: 219-228.   DOI   ScienceOn
5 Shoseyov, O., Z. Shani, and I. Levy. 2006. Carbohydrate binding modules: Biochemical properties and novel applications. Microbiol. Mol. Biol. Rev. 70: 283-295.   DOI   ScienceOn
6 Souza, T. A., C. R. Santos, A. R. Souza, D. P. Oldiges, R. Ruller, R. A. Prade, et al. 2011. Structure of a novel thermostable GH51 ${\alpha}$-L-arabinofuranosidase from Thermotoga petrophila RKU-1. Protein Sci. 20: 1632-1637.   DOI   ScienceOn
7 Taylor, E. J., N. L. Smith, J. P. Turkenburg, S. D'Souza, H. J. Gilbert, and G. J. Davies. 2006. Structural insight into the ligand specificity of a thermostable family 51 arabinofuranosidase, Araf51, from Clostridium thermocellum. Biochem. J. 395: 31-37.   DOI   ScienceOn
8 Yoon, H. S., I. Keum, N. S. Han, and J. H. Kim. 2004. Molecular cloning and characterization of a gene encoding ${\alpha}$-Larabinofuranosidase from Thermotoga maritima. Food Sci. Biotechnol. 13: 244-247.
9 Cantarel, B. L., P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat. 2009. The Carbohydrate-Active EnZymes database (CAZy): An expert resource for glycogenomics. Nucleic Acids Res. 37: 233-238.   DOI   ScienceOn
10 CCP4. 1994. The CCP4 suite: Programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50: 760-763.   DOI   ScienceOn
11 Davies, G. J., K. S. Wilson, and B. Henrissat. 1997. Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem. J. 321: 557-559.
12 Holm, L. and J. Park. 2000. Dali: Lite workbench for protein structure comparison. Bioinformatics 16: 566-567.   DOI   ScienceOn
13 Emsley, P. and K. Cowtan. 2004. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60: 2126-2132.   DOI   ScienceOn
14 Gilead, S. and Y. Shoham. 1995. Purification and characterization of ${\alpha}$-L-arabinofuranosidase from Bacillus stearothermophilus T-6. Appl. Environ. Microbiol. 61: 170-174.
15 Henrissat, B. and G. Davies. 1997. Structural and sequencebased classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 7: 637-644.   DOI   ScienceOn
16 Hovel, K., D. Shallom, K. Niefind, V. Belakhov, G. Shoham, T. Baasov, Y. Shoham, and D. Schomburg. 2003. Crystal structure and snapshots along the reaction pathway of a family 51 ${\alpha}$-Larabinofuranosidase. EMBO J. 22: 4922-4932.   DOI   ScienceOn
17 Im, D. H., K. Kimura, F. Hayasaka, T. Tanaka, M. Noguchi, A. Kobayashi, et al. 2012. Crystal structures of glycoside hydrolase family 51 ${\alpha}$-L-arabinofuranosidase from Thermotoga maritima. Biosci. Biotechnol. Biochem. 76: 423-428.   DOI   ScienceOn
18 Jones, T. A., J. Y. Zou, S. W. Cowan, and M. Kjeldgaard. 1991. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47: 110-119.   DOI   ScienceOn
19 McCoy, A. J., R. W. Grosse-Kunstleve, P. D. Adams, M. D. Winn, L. C. Storoni, and R. J. Read. 2007. Phaser crystallographic software. J. Appl. Crystallogr. 40: 658-674.   DOI   ScienceOn
20 Miller, G. L. 1959. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Anal. Chem. 31: 426-428.   DOI
21 Park, J. M., N. S. Han, and T. J. Kim. 2007. Rapid detection and isolation of known and putative alpha-L-arabinofuranosidase genes using degenerate PCR primers. J. Microbiol. Biotechnol. 17: 481-489.
22 Numan, M. T. and N. B. Bhosle. 2006. Alpha-L-arabinofuranosidases: The potential applications in biotechnology. J. Ind. Microbiol. Biotechnol. 33: 247-260.   DOI   ScienceOn
23 Paes, G., L. K. Skov, L. K. O'Donohue, C. Remond, L. K. Kastrup, M. Gajhede, and O. Mirza. 2008. The structure of the complex between a branched pentasaccharide and Thermobacillus xylanilyticus GH-51 arabinofuranosidase reveals xylan-binding determinants and induced fit. Biochemistry 47: 7441-7451.   DOI   ScienceOn