Enhancing the activity of Bacillus circulans xylanase by modulating the flexibility of the hinge region

Journal of Industrial Microbiology and Biotechnology

Volumn 41, Issue 8, 2014, Pages 1181-1190

  Kazuyo, Fukura ^a   Hong, So Yeon ^a   Yeon, Young Joo ^a   Joo, Jeong Chan ^a,b   Yoo, Young Je ^a  

^a Seoul National University   (South Korea)

^b UNIVERSITY OF TORONTO   (Canada)

Author keywords

Activity; Dynamics; Flexibility; Hinge; Xylanase

Indexed keywords

AMINO ACID; ENDO 1,4 BETA XYLANASE; PRIMER DNA;

BACILLUS; BIOMECHANICS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; GENETICS; KINETICS; METABOLISM; PROTEIN CONFORMATION; SITE DIRECTED MUTAGENESIS;

AMINO ACIDS; BACILLUS; BIOMECHANICAL PHENOMENA; DNA PRIMERS; ENDO-1,4-BETA XYLANASES; KINETICS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; PROTEIN CONFORMATION;

EID: 84905098144     PISSN: 13675435     EISSN: 14765535     Source Type: Journal    
DOI: 10.1007/s10295-014-1454-z     Document Type: Article

References (28)

1. Bailey MJ, Biely P, Poutanen K (1992) Interlaboratory testing of methods for assay of xylanase activity. J Biotechnol 23(3):257-270
2. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein dye binding. Anal Biochem 72(1-2):248-254
3. Fisher CL, Pei GK (1997) Modification of a PCR-based site-directed mutagenesis method. Biotechniques 23(4):570-574 (Pubitemid 27450899)
4. Frey PA (2001) Strong hydrogen bonding in molecules and enzymatic complexes. Magn Reson Chem 39((Spec. Iss.)):S190-S198
5. Hammes GG (2002) Multiple conformational changes in enzyme catalysis. Biochemistry 41(26):8221-8228
6. Hayward S (1999) Structural principles governing domain motions in proteins. Proteins Struct Funct Genet 36(4):425-435
7. Hayward S, Berendsen HJC (1998) Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins Struct Funct Genet 30(2):144-154 (Pubitemid 28080149)
8. Joo JC, Pack SP, Kim YH, Yoo YJ (2011) Thermostabilization of Bacillus circulans xylanase: computational optimization of unstable residues based on thermal fluctuation analysis. J Biotechnol 151(1):56-65
9. Kim T, Joo JC, Yoo YJ (2012) Hydrophobic interaction network analysis for thermostabilization of a mesophilic xylanase. J Biotechnol 161(1):49-59
10. Krivov GG, Shapovalov MV, Dunbrack RL Jr (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins Struct Funct Bioinform 77(4):778-795
11. Lineweaver H, Burk D (1934) The determination of enzyme dissociation constants. J Am Chem Soc 56(3):658-666
12. Ludwiczek ML, Heller M, Kantner T, McIntosh LP (2007) A Secondary xylan-binding site enhances the catalytic activity of a single-domain family 11 glycoside hydrolase. J Mol Biol 373(2):337-354 (Pubitemid 47445568)
13. Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 11(2):184-197 (Pubitemid 34075781)
14. Muilu J, Törrönen A, Peräkylä M, Rouvinen J (1998) Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study. Proteins Struct Funct Genet 31(4):434-444 (Pubitemid 28265560)
15. Plesniak LA, Wakarchuk WW, McIntosh LP (1996) Secondary structure and NMR assignments of Bacillus circulans xylanase. Protein Sci 5(6):1118-1135 (Pubitemid 26172900)
16. Pollet A, Vandermarliere E, Lammertyn J, Strelkov SV, Delcour JA, Courtin CM (2009) Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases. Proteins Struct Funct Bioinform 77(2):395-403
17. Potestio R, Pontiggia F, Micheletti C (2009) Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits. Biophys J 96(12):4993-5002
18. Radivojac P, Obradovic Z, Smith DK, Zhu G, Vucetic S, Brown CJ, Lawson JD, Dunker AK (2004) Protein flexibility and intrinsic disorder. Protein Sci 13(1):71-80 (Pubitemid 38021142)
19. Schein CH, Noteborn MHM (1988) Formation of soluble recombinant proteins in Escherichia coli is favored by lower growth temperature. BioTechnology 6(3):291-294
20. Schramm AM, Mehra-Chaudhary R, Furdui CM, Beamer LJ (2008) Backbone flexibility, conformational change, and catalysis in a phosphohexomutase from Pseudomonas aeruginosa. Biochemistry 47(35):9154-9162
21. Schulz GE (1991) Domain motions in proteins. Curr Opin Struct Biol 1(6):883-888
22. Sime JT (1999) Applications of biocatalysis to industrial processes. J Chem Educ 76(12):1658-1661
23. Subramaniyan S, Prema P (2002) Biotechnology of microbial xylanases: enzymology, molecular biology, and application. Crit Rev Biotechnol 22(1):33-64 (Pubitemid 34272292)
24. Sung WL, Luk CK, Zahab DM, Wakarchuk W (1993) Overexpression of the Bacillus subtilis and circulans xylanases in Escherichia coli. Protein Expr Purif 4(3):200-206
25. Tina KG, Bhadra R, Srinivasan N (2007) PIC: protein interactions calculator. Nucleic Acids Res 35(Suppl.2):W473-W476
26. Wells S, Menor S, Hespenheide B, Thorpe MF (2005) Constrained geometric simulation of diffusive motion in proteins. Phys Biol 2(4):S127-S136 (Pubitemid 41609439)
27. Yon JM, Perahia D, Ghélis C (1998) Conformational dynamics and enzyme activity. Biochimie 80(1):33-42 (Pubitemid 28211651)
28. Zheng L, Baumann U, Reymond JL (2004) An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32(14):e115