A rational design for trypsin-resistant improvement of Armillariella tabescens β-mannanase MAN47 based on molecular structure evaluation

Journal of Biotechnology

Volumn 163, Issue 4, 2013, Pages 401-407

  Li, Yufeng ^a   Hu, Fengjuan ^a,c   Wang, Xuman ^a   Cao, Hong ^a   Liu, Daling ^a   Yao, Dongsheng ^a,b  

^a JINAN UNIVERSITY   (China)

^b National Engineering Research Center of Genetic Medicine   (China)

^c Biothera Solutions Formerly as Sinoasis Pharma Ltd   (China)

Author keywords

Homology modeling; Overlap extension PCR; Protease resistance; Site directed mutagenesis

Indexed keywords

COMPUTATIONAL DESIGN; DIGESTIVE TRACT; FEED INDUSTRIES; HALF LIVES; HOMOLOGY MODELING; MANNANASE; MOLECULAR DYNAMICS SIMULATIONS; OVERLAP-EXTENSION PCR; PROTEASE-RESISTANCE; RATIONAL DESIGN; RATIONAL METHODS; SITE DIRECTED MUTAGENESIS; STRUCTURE EVALUATIONS; THREE DIMENSIONAL SPACE; TRIPLE MUTANTS; WILD-TYPE ENZYMES;

CATALYST ACTIVITY; DIGESTIVE SYSTEM; ENZYME ACTIVITY; MOLECULAR DYNAMICS;

MOLECULAR STRUCTURE;

BETA MANNOSIDASE; MUTANT PROTEIN; PROTEINASE; TRYPSIN;

ARMILLARIELLA TABESCENS; ARTICLE; CATALYSIS; CHEMICAL STRUCTURE; ENZYME ACTIVITY; EVALUATION; HALF LIFE TIME; HYDROGEN BOND; MICROORGANISM; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; PREDICTION; PRIORITY JOURNAL; SEQUENCE HOMOLOGY; SIMULATION; WILD TYPE;

ARMILLARIA; BETA-MANNOSIDASE; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, FUNGAL; ESCHERICHIA COLI; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; MUTAGENESIS, SITE-DIRECTED; MUTATION; PROTEIN ENGINEERING; TRYPSIN;

ARMILLARIELLA TABESCENS;

EID: 84874313506     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.12.018     Document Type: Article

References (34)

1. Arnold K., Bordoli L., Kopp J., Schwede T. The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22:195-201.
2. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry 1982, 4(2):187-217.
3. Cao Y.N., Wang Y.R., Meng K., Bai Y.G., Shi P.J., Luo H.Y., Yang P.L., Zhou Z.G., Zhang Z.F., Yao B. A novel protease-resistant α-galactosidase with high hydrolytic activity from Gibberella sp: F75: gene cloning, expression, and enzymatic characterization. Applied Microbiology and Biotechnology 2009, 3:875-884.
4. Dhawan S., Kaur J. Microbial mannanases: an overview of production and applications. Critical Reviews in Biotechnology 2007, 27:197-216.
5. Fu D.W., Li Z.Y., Huang H.Q., Yuan T.Z., Shi P.J., Luo H.Y., Meng K., Yang P.L., Yao B. Catalytic efficiency of HAP phytases is determined by a key residue in close proximity to the active site. Applied Microbiology and Biotechnology 2011, 10.1007/s00253-011-3171-0.
6. Gonzalez-Segura L., Velasco-Garcia R., Rudińo-Pińera E., Mújica-Jiménez C. Site-directed mutagenesis and homology modeling indicate an important role of cysteine439 in the stability of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa. Biochimie 2005, 87:1056-1064.
7. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modelling. Electrophoresis 1997, 18:2714-2723.
8. He Y.Z., Fan K.Q., Jia C.J., Wang Z.J., Pan W.B., Huang L., Yang K.Q., Dong Z.Y. Characterization of a hyperth ermostable Fe-superoxide dismutase from hot spring. Applied Microbiology and Biotechnology 2007, 75:367-376.
9. Hsiao H.Y., Anderson D.M., Dale N.M. Levels of β-mannan in soybean meal. Poultry Science 2006, 85:1430-1432.
10. Ibdah M., Bar-Ilan A., Livnah O., Schloss J.V., Barak Z., Chipman D.M. Homology modeling of the structure of bacterial acetohydroxy acid synthase and examination of the active site by site-directed mutagenesis. Biochemistry 1996, 35:16282-16291.
11. Katrolia P., Jia H., Yan Q., Song S., Jiang Z., Xu H. Characterization of a protease-resistant α-galactosidase from the thermophilic fungus Rhizomucor miehei and its application in removal of raffinose family oligosaccharides. Bioresource Technology 2012, 110:578-586.
12. Kiarie E., Nyachoti C.M., Slominski B.A., Blank G. Growth performance, gastrointestinal microbial activity, and nutrient digestibility in early-weaned pigs fed diets containing flaxseed and carbohydrase enzyme. Journal of Animal Science 2007, 85:2982-2993.
13. Kim D., Choi K.Y., Yoo M., Choi J.N., Lee C.H., Zylstra G.J., Kang B.S., Kim E. Benzylic and aryl hydroxylations of m-xylene by o-xylene dioxygenase from Rhodococcus sp. strain DK17. Applied Microbiology and Biotechnology 2010, 86:1841-1847.
14. Klepeis J.L., Lindorff-Larsen K., Dror R.O., Shaw D.E. Long-timescale molecular dynamics simulations of protein structure and function. Current Opinion in Structural Biology 2009, 19:120-127.
15. Lin W.J., Chan M., Goh L.L., Sim T.S. Molecular basis for thermal properties of Streptomyces thermovulgaris fumarase C hinge at hydrophilic amino acids R163 E170 and S347. Applied Microbiology Biotechnology 2007, 75:329-333.
16. Luo H.Y., Wang Y.R., Wang H. A novel highly acidic β-mannanase from the acidophilic fungus Bispora sp. MEY-1: gene cloning and overexpression in Pichia pastoris. Applied Microbiology and Biotechnology 2009, 82:453-461.
17. Lv, X.H., 2010. Armillariella tabescens EJLY2098 MAN47 β-mannanase: in vitro directed evolution and structural analysis. Dissertation. Jinan University.
18. Maiorov V.N., Crippen G.M. Significance of root-mean-square deviation in comparing three-dimensional structures of globular proteins. Journal of Molecular Biology 1994, 235:625-634.
19. Miller G.L. Use of dinitrosalicylic acid reagent for determination of reducing sugar. Analytical Chemistry 1959, 31:426-428.
20. Ogola H.J.O., Hashimoto N., Miyabe S., Ashida H., Ishikawa T., Shibata H., Sawa Y. Enhancement of hydrogen peroxide stability of a novel Anabaena sp. DyP-type peroxidase by site-directed mutagenesis of methionine residues. Applied Microbiology and Biotechnology 2010, 87:1727-1736.
21. Pham T.A., Berrin J.G., Record E., Recorda K., Tob K.A., Sigoillota J.C. Hydrolysis of softwood by Aspergillus mannanase: role of a carbohydrate-binding module. Journal of Biotechnology 2010, 148:163-170.
22. Reva B.A., Finkelstein A.V., Skolnick J. What is the probability of a chance prediction of a protein structure with an rmsd of 6Å?. Folding & Design 1998, 3:141-147.
23. Sabini E., Schubert H., Murshudov G., Wilson K.S., Siika-Ahob M., Penttila M. The three dimensional structure of a Trichoderma reesei β-mannanase from glycoside hydrolase family 5. Acta Crystallographica 2000, 56:3-13.
24. Sali A., Potterton L., Yuan F., vanVlijmen H., Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins 1995, 23:318-326.
25. Schwede T., Kopp J., Guex N., et al. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Research 2003, 31(13):3381-3385.
26. Storbeck K.H., Swart P., Swart A.C. Cytochrome P450 side-chain cleavage: insights gained from homology modeling. Molecular and Cellular Endocrinology 2007, 265/266:65-70.
27. Tian J., Wang P., Gao S., Chu X., Wu N., Fan Y. Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation. FEBS Journal 2010, 277:4901-4908.
28. Wang Y.F., Wong A.H.H., Huang X.K., Liu D.L., Yao D.S. Cloning, expression and characterization of mannanase from Armillariella tabescens EJLY2098 in Pichia pastoris. Chinese Journal of Biotechnology 2009, 25(6):920-926.
29. Yáñez J.L., Beltranena E., Cervantes M., Zijlstra R.T. Effect of phytase and xylanase supplementation or particle size on nutrient digestibility of diets containing distillers dried grains with solubles cofermented from wheat and corn in ileal-cannulated grower pigs. Journal of Animal Science 2011, 89:113-123.
30. Yeom S.J., Seo E.S., Kim Y.S., Oh D.K. Increased d-allose production by the R132E mutant of ribose-5-phosphate isomerase from Clostridium thermocellum. Applied Microbiology and Biotechnology 2011, 89:1859-1866.
31. Zahura U.A., Rahman M.M., Inoue A., Tanaka H., Ojima T. An endo-β-1,4-mannanase, AkMan, from the common sea hare Aplysia kurodai. Comparative Biochemistry and Physiology, Part B 2010, 157:137-143.
32. Zhang W.M., Le X.G. Cumulative improvements of thermostability and pH-activity profile of Aspergillus niger PhyA phytase by site-directed mutagenesis. Applied Microbiology and Biotechnology 2008, 77:1033-1040.
33. Zhang H.F., Lountos G.T., Ching C.B., Jiang R. Engineering of glycerol dehydrogenase for improved activity towards 1, 3-butanediol. Applied Microbiology and Biotechnology 2010, 88:117-124.
34. Zou X.T., Qiao X.J., Xu Z.R. Effect of β-mannanase (hemicell) on growth performance and immunity of broilers. Poultry Science 2006, 85:2176-2179.