Skip to main content
SpringerLink
Log in

Cloning, molecular modeling, and docking analysis of alkali-thermostable β-mannanase from Bacillus nealsonii PN-11

  • Biotechnologically relevant enzymes and proteins
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

An alkali-thermostable β-mannanase gene from Bacillus nealsonii PN-11 was cloned by functional screening of E. coli cells transformed with pSMART/HaeIII genomic library. The ORF encoding mannanase consisted of 1100 bp, corresponding to protein of 369 amino acids and has a catalytic domain belonging to glycoside hydrolase family 5. Cloned mannanase was smaller in size than the native mannanase by 10 kDa. This change in molecular mass could be because of difference in the glycosylation. The tertiary structure of the β-mannanase (MANPN11) was designed and it showed a classical (α/β) TIM-like barrel motif. Active site of MANPN11 was represented by 8 amino acid residues viz., Glu152, Trp189, His217, Tyr219, Glu247, Trp276, Trp285, and Tyr287. Model surface charge of MANPN11 predicted that surface near active site was mostly negative, and the opposite side was positive which might be responsible for the stability of the enzymes at high pH. Stability of MANPN11 at alkaline pH was further supported by the formation of a hydrophobic pocket near active site of the enzyme. To understand the ability of MANPN11 to bind with different substrates, docking studies were performed and found that mannopentose fitted properly into active site and form stable enzyme substrate complex.

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

Access this article

Log in via an institution

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  • Akita M, Takeda N, Hirasawa K, Sakai H, Kawamoto M, Yamamoto M, Grant WD, Hatada Y, Ito S, Horikoshi K (2004) Crystallization and preliminary X-ray study of alkaline mannanase from an alkaliphilic Bacillus isolate. Acta Crystallogr D Biol Crystallogr 60:1490–1492

    Article  PubMed  Google Scholar 

  • Ausubel FM, Brent R, Kingston RE, Moore DD, Seidmann JD, Smith JA, Struhl K (2006) Current Protocols in Molecular Biology, Vol 1, Greene Publishing Association, Wiley-Interscience, New York

  • Chauhan PS, Puri N, Sharma P, Gupta N (2012) Mannanases: microbial sources, production, properties and potential biotechnological applications. Appl Microbiol Biotechnol 93:1817–1830

    Article  CAS  PubMed  Google Scholar 

  • Chauhan PS, George N, Sondhi S, Puri N, Gupta N (2014a) An overview of purification strategies for microbial mannanases. Int J Pharm Bio Sci 5:176–192

    CAS  Google Scholar 

  • Chauhan PS, Soni SK, Sharma P, Saini A, Gupta N (2014b) A mannanase from Bacillus nealsonii PN-11: statistical optimization of production and application in biobleaching of pulp in combination with xylanase. Int J Pharma Bio Sci 5:237–251

    CAS  Google Scholar 

  • Chauhan PS, Bharadwaj A, Puri N, Gupta N (2014c) Optimization of medium composition for alkali-thermostable mannanase production by Bacillus nealsonii PN-11 in submerged fermentation. Int J Curr Microbiol Appl Sci 3:1033–1045

    CAS  Google Scholar 

  • Chauhan PS, Sharma P, Puri N, Gupta N (2014d) Purification and characterization of an alkali-thermostable β-Mannanase from Bacillus nealsonii PN-11 and its application in manno-oligosaccharides preparation having prebiotic potential. Eur Food Res Technol 238:927–936

    Article  CAS  Google Scholar 

  • Chauhan PS, Sharma P, Puri N, Gupta N (2014e) A process for reduction in viscosity of coffee extract by enzymatic hydrolysis of mannan. Bioprocess Biosyst Eng 3:1459–67

    Article  Google Scholar 

  • Corpet F (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res 16:10881–10890

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Coughlan S, Wang XG, Britton KL, Stillman TJ, Rice DW, Chiaraluce R, Consalvi V, Scandurra R, Engel PC (2001) Contribution of an aspartate residue, D114, in the active site of clostridial glutamate dehydrogenase to the enzyme’s unusual pH dependence. Biochim Biophys Acta 1544:10–17

    Article  CAS  PubMed  Google Scholar 

  • Dell A, Galadari A, Sastre F, Hitchen P (2011) Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes. Int J Microbiol. doi:10.1155/2010/148178

    PubMed Central  Google Scholar 

  • Fang TY, Ford C (1998) Protein engineering of Aspergillus awamori glucoamylase to increase its pH optimum. Protein Eng 11:383–388

    Article  CAS  PubMed  Google Scholar 

  • Gálvez CA, Ospina JV, Sanchez PG, Zornosa RA (2013) Cloning and biochemical characterization of an endo-1,4-β-mannanase from the coffee berry borer Hypothenemus hampei. BMC Res Notes 6:333. doi:10.1186/1756-0500-6-333

    Article  Google Scholar 

  • George N, Chauhan PS, Puri N, Gupta N (2014a) Statistical optimization of process parameters for production of alkaline protease from Vibrio metschnikovii NG155 having application in leather industry. Int J Pharma Bio Sci 5:509–517

    Google Scholar 

  • George N, Chauhan PS, Kumar V, Puri N, Gupta N (2014b) An approach to ecofriendly leather: lime and sulphide free dehairing of skin and hide using bacterial alkaline protease at industrial scale. J Clean Prod 79:249–257

    Article  CAS  Google Scholar 

  • Ghosh A, Luís AS, Brás JLA, Fontes CMGA, Goyal A (2013) Thermostable recombinant β(1→4)-mannanase from C. thermocellum: biochemical characterization and manno-oligosaccharides production. J Agric Food Chem 61:12333–12344

    Article  CAS  PubMed  Google Scholar 

  • Hakamada Y, Ohkubo Y, Ohashi S (2014) Purification and characterization of β-mannanase from Reinekea sp. KIT-YO10 with transglycosylation activity. Biosci Biotechnol Biochem. doi:10.1080/09168451.2014.895658

    PubMed  Google Scholar 

  • Hatada Y, Takeda N, Hirasawa K, Ohta Y, Usami R, Yoshida Y, Ito S, Horikoshi K (2005) Sequence of the gene for a high-alkaline mannanase from an alkaliphilic Bacillus sp. strain JAMB-750, its expression in B. subtilis and characterization of the recombinant enzyme. Extremophiles 9:497–500

    Article  CAS  PubMed  Google Scholar 

  • He X, Liu N, Zhang Z, Zhang B, Ma Y (2008) Inducible and constitutive expression of a novel thermo stable alkaline β-mannanase from alkalophilic Bacillus sp. N16-5 in Pichia pastoris and characterization of the recombinant enzyme. Enzyme Microb Technol 43:13–18

    Article  CAS  Google Scholar 

  • Kumar L, Dutt D, Tapas S, Kumar P (2013) Purification and biochemical characterization, homology modeling and active side binding mode interaction of thermo-alkali-stable β-1,4 endoxylanase from Coprinus cinerus LK-D-NCIM-1369. Biocat Agric Biotechnol 2:267–277

    Google Scholar 

  • Lv J, Chen Y, Pei H, Yang W, Li Z, Dong B, Cao Y (2013) Cloning, expression, and characterization of β-mannanase from Bacillus subtilis MAFIC-S11 in Pichia pastoris. Appl Biochem Biotechnol 169:2326–2340. doi:10.1007/s12010-013-0156-8

    Article  CAS  PubMed  Google Scholar 

  • Mamo G, Thunnissen M, Kaul R, Mattiasson B (2009) An alkaline active xylanase: insights into mechanisms of high pH catalytic adaptation. Biochimie 91:1187–1196

    Article  CAS  PubMed  Google Scholar 

  • Santos CR, Paiva JH, Meza AN, Cota J, Alvarez TM, Ruller R, Prade RA, Squina FM, Murakami MT (2012) Molecular insights into substrate specificity and thermal stability of a bacterial GH5-CBM27 endo-1,4-β-D-mannanase. J Struct Biol 177:469–76

    Article  PubMed  Google Scholar 

  • Shirai T, Ishida H, Noda J, Yamane T, Ozaki K, Hakamada Y, Ito S (2001) Crystal structure of alkaline cellulase K: insight into the alkaline adaptation of an industrial enzyme. J Mol Biol 310:1079–1087

    Article  CAS  PubMed  Google Scholar 

  • Singh RP, Rai AR, Choudhury KR, Dubey RC (2011) Homology modeling and sequence analysis of a highly thermostable endo-(1,4)-beta-mannanase from the marine bacterium Rhodothermus marinus. Int J App Sci Environ Sanit 6:485–494

    CAS  Google Scholar 

  • Sondhi S, Sharma P, George N, Chauhan PS, Puri N, Gupta N (2014) A novel extracellular thermo-alkali-stable laccase from Bacillus tequilensis SN4 having potential to biobleach softwood pulp. 3Biotech. doi:10.1007/s13205-014-0207-z

    Google Scholar 

  • Stoll D, LeNours J, Anderson L, Stalbrand H, Loleggio L (2005) The structure and characterization of a modular endo-β-1,4-mannanase from Cellulomonas fimi. Biochemistry 44:12700–12708

    Article  PubMed  Google Scholar 

  • Wang Y, Vilaplana F, Brumer H, Aspeborg H (2014) Enzymatic characterization of a glycoside hydrolase family 5 subfamily 7 (GH5-7) mannanase from Arabidopsis thaliana. Planta 239:653–665

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yoshida S, Sako Y, Uchida A (1998) Cloning, sequence analysis, and expression in Escherichia coli of a gene coding for an enzyme from Bacillus circulans K-1 that degrades guar gum. Biosci Biotechnol Biochem 62:514–520

    Article  CAS  PubMed  Google Scholar 

  • Zacharius RM, Zell TE, Morrison JH, Woodlock JJ (1969) Glycoprotein staining following electrophoresis on acrylamide gels. Anal Biochem 30:148–152

    Article  CAS  PubMed  Google Scholar 

  • Zhao Y, Zhang Y, Cao Y, Qi J, Mao L, Xue Y, Gao F, Peng H, Wang X, Gao GF, Ma Y (2011) Structural analysis of alkaline β-mannanase from alkaliphilic Bacillus sp. N16-5: implications for adaptation to alkaline conditions. Plos One 6(1):e14608. doi:10.1371/journal.pone.0014608

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

Prakram Singh Chauhan is thankful to Council of Scientific and Industrial Research (CSIR), New Delhi, India, for providing a Senior Research Fellowship.

Conflict of interest

The authors declare no competing financial interest.

Author information

Authors and Affiliations

  1. Department of Microbiology, BMS Block, Panjab University South Campus, Chandigarh, India

    Prakram Singh Chauhan, Prince Sharma & Naveen Gupta

  2. Department of Pharmacoinformatics, National Institute of Pharmaceutical Science Education and Research, S.A.S, Nagar, Mohali, Punjab, India

    Satya Prakash Tripathi & Abhays T. Sangamwar

  3. Department of Industrial Microbiology, Guru Nanak Khalsa College, Yamunanagar, Haryana, India

    Neena Puri

Authors
  1. Prakram Singh Chauhan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Satya Prakash Tripathi
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Abhays T. Sangamwar
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Neena Puri
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Prince Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Naveen Gupta
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Prince Sharma or Naveen Gupta.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 423 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Chauhan, P.S., Tripathi, S.P., Sangamwar, A.T. et al. Cloning, molecular modeling, and docking analysis of alkali-thermostable β-mannanase from Bacillus nealsonii PN-11. Appl Microbiol Biotechnol 99, 8917–8925 (2015). https://doi.org/10.1007/s00253-015-6613-2

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-015-6613-2

Keywords

Search

Navigation