Skip to main content
Log in

Three-dimensional structure of an alkaline xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5 and improvement of its thermal performance by introducing arginines substitutions

  • Original Research Paper
  • Published:
Biotechnology Letters Aims and scope Submit manuscript

Abstract

The alkaline xylanase Xyn11A-LC from the alkalophilic Bacillus sp. SN5 was expressed in E. coli, purified and crystallized. The crystal structure was determined at a resolution of 1.49 Å. Xyn11A-LC has the β-jelly roll structure typical of family 11 xylanases. To improve its thermostability and thermophilicity, a mutant SB3 was constructed by introducing three arginines on the different sides of the protein surface. SB3 increased the optimum temperature by 5 °C. The wild type and SB3 had the half-lives of 22 and 68 min at 65 °C at pH 8.0 (Tris/HCl buffer), respectively. CD spectroscopy revealed that the melting temperature (T m) of the wild type and SB3 were 55.3 and 66.9 °C, respectively. These results showed that the introduction of arginines enhance the thermophilicity and thermostability of Xyn11A-LC.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  • Argos P, Rossman MG, Grau UM, Zuber H, Frank G, Tratschin JD (1979) Thermal stability and protein structure. Biochemistry 18:5698–5703

    Article  CAS  PubMed  Google Scholar 

  • Bai WQ, Xue YF, Zhou C, Ma YH (2012) Cloning, expression and characterization of a novel salt-tolerant xylanase from Bacillus sp SN5. Biotechnol Lett 34:2093–2099

    Article  CAS  PubMed  Google Scholar 

  • Borders CL Jr, Broadwater JA, Bekeny PA, Salmon JE, Lee AS, Eldridge AM, Pett VB (1994) A structural role for arginine in proteins: multiple hydrogen bonds to backbone carbonyl oxygens. Protein Sci 3:541–548

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921

    Article  CAS  PubMed  Google Scholar 

  • Chan CH, Yu TH, Wong KB (2011) Stabilizing salt-bridge enhances protein thermostability by reducing the heat capacity change of unfolding. PLoS ONE 6:e21624

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Collins T, Gerday C, Feller G (2005) Xylanases, xylanase families and extremophilic xylanases. FEMS Microbiol Rev 29:3–23

    Article  CAS  PubMed  Google Scholar 

  • Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132

    Article  PubMed  Google Scholar 

  • Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-Pdb-Viewer: an environment for comparative protein modelling. Electrophoresis 18:2714–2723

    Article  CAS  PubMed  Google Scholar 

  • Hakulinen N, Turunen O, Janis J, Leisola M, Rouvinen J (2003) Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. Eur J Biochem 270:1399–1412

    Article  CAS  PubMed  Google Scholar 

  • Harris GW, Pickersgill RW, Connerton I, Debeire P, Touzel JP, Breton C, Perez S (1997) Structural basis of the properties of an industrially relevant thermophilic xylanase. Proteins 29:77–86

    Article  CAS  PubMed  Google Scholar 

  • Joshi MD, Sidhu G, Pot I, Brayer GD, Withers SG, McIntosh LP (2000) Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the pH optimum of a glycosidase. J Mol Biol 299:255–279

    Article  CAS  PubMed  Google Scholar 

  • Kumar S, Tsai CJ, Nussinov R (2000) Factors enhancing protein thermostability. Protein Eng 13:179–191

    Article  CAS  PubMed  Google Scholar 

  • Lam S, Yeung R, Yu T, Sze K, Wong K (2011) A rigidifying salt-bridge favors the activity of thermophilic enzyme at high temperatures at the expense of low-temperature activity. PLoS Biol 9:e1001027

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lu N, Moriyama H, Nakamura S, Sato T, Tanaka N (2000) Crystallization and initial X-ray analysis of alkaline xylanase. Acta Crystallogr D Biol Crystallogr 56:464–465

    Article  CAS  PubMed  Google Scholar 

  • Matsutani M, Hirakawa H, Nishikura M, Soemphol W, Ali IA, Yakushi T, Matsushita K (2011) Increased number of Arginine-based salt bridges contributes to the thermotolerance of thermotolerant acetic acid bacteria, Acetobacter tropicalis SKU1100. Biochem Biophys Res Commun 409:120–124

    Article  CAS  PubMed  Google Scholar 

  • Mccoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, Read RJ (2007) Phaser crystallographic software. J Appl Crystallogr 40:658–674

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mrabet NT, Van den Broeck A, Van den brande I, Stanssens P, Laroche Y, Lambeir AM, Matthijssens G, Jenkins J, Chiadmi M, van Tilbeurgh H et al (1992) Arginine residues as stabilizing elements in proteins. Biochemistry 31:2239–2253

    Article  CAS  PubMed  Google Scholar 

  • Otwinowski z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth Enzymol 276:307–326

    Article  CAS  Google Scholar 

  • Strub C, Alies C, Lougarre A, Ladurantie C, Czaplicki J, Fournier D (2004) Mutation of exposed hydrophobic amino acids to arginine to increase protein stability. BMC Biochem 5:9

    Article  PubMed Central  PubMed  Google Scholar 

  • Torronen A, Rouvinen J (1997) Structural and functional properties of low molecular weight endo-1, 4-beta-xylanases. J Biotechnol 57:137–149

    Article  CAS  PubMed  Google Scholar 

  • Torronen A, Harkki A, Rouvinen J (1994) Three-dimensional structure of endo-1,4-beta-xylanase II from Trichoderma reesei: two conformational states in the active site. EMBO J 13:2493–2501

    CAS  PubMed Central  PubMed  Google Scholar 

  • Turunen O, Etuaho K, Fenel F, Vehmaanpera J, Wu X, Rouvinen J, Leisola M (2001) A combination of weakly stabilizing mutations with a disulfide bridge in the alpha-helix region of Trichoderma reesei endo-1, 4-beta-xylanase II increases the thermal stability through synergism. J Biotechnol 88:37–46

    Article  CAS  PubMed  Google Scholar 

  • Turunen O, Vuorio M, Fenel F et al (2002) Engineering of multiple arginines into the Ser/Thr surface of Trichoderma reesei endo-1, 4-beta-xylanase II increases the thermotolerance and shifts the pH optimum towards alkaline pH. Protein Eng 15:141–145

    Article  CAS  PubMed  Google Scholar 

  • Umemoto H, Ihsanawati, Inami M, Yatsunami R, Fukui T, Kumasaka T, Tanaka N, Nakamura S (2009) Improvement of alkaliphily of Bacillus alkaline xylanase by introducing amino acid substitutions both on catalytic cleft and protein surface. Biosci Biotech Bioch 73:965–967

    Article  CAS  Google Scholar 

  • Vogt G, Woell S, Argos P (1997) Protein thermal stability, hydrogen bonds, and ion pairs. J Mol Biol 269:631–643

    Article  CAS  PubMed  Google Scholar 

  • Wang Y, Fu Z, Huang H, Zhang H, Yao B, Xiong H, Turunen O (2012) Improved thermal performance of Thermomyces lanuginosus GH11 xylanase by engineering of an N-terminal disulfide bridge. Bioresour Technol 112:275–279

    Article  CAS  PubMed  Google Scholar 

  • Zhang S, Zhang K, Chen X, Chu X, Sun F, Dong Z (2010) Five mutations in N-terminus confer thermostability on mesophilic xylanase. Biochem Biophys Res Commun 395:200–206

    Article  CAS  PubMed  Google Scholar 

  • Zhou C, Xue Y, Ma Y (2010) Enhancing the thermostability of alpha-glucosidase from Thermoanaerobacter tengcongensis MB4 by single proline substitution. J Biosci Bioeng 110:12–17

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This study was supported by the National Basic Research Program of China (2011CBA00800 and 2009CB724700), Chinese National Programs for High Technology Research and Development (2011AA02A206 and 2012AA022100) and the Knowledge Innovative Program of Chinese Academy of Science (KSCX2-EW-G-8).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Yanhe Ma.

Electronic supplementary material

Supporting information

Supplementary Table 1: Data collection and refinement statistics for Xyn11A-LC

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 55 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Bai, W., Zhou, C., Xue, Y. et al. Three-dimensional structure of an alkaline xylanase Xyn11A-LC from alkalophilic Bacillus sp. SN5 and improvement of its thermal performance by introducing arginines substitutions. Biotechnol Lett 36, 1495–1501 (2014). https://doi.org/10.1007/s10529-014-1512-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10529-014-1512-7

Keywords

Navigation