Engineering lower inhibitor affinities in β-D-xylosidase

Applied Microbiology and Biotechnology

Volumn 86, Issue 4, 2010, Pages 1099-1113

  Fan, Zhanmin ^a   Yuan, Ling ^a   Jordan, Douglas B ^b   Wagschal, Kurt ^c   Heng, Chamroeun ^c   Braker, Jay D ^b  

^a UNIVERSITY OF KENTUCKY   (United States)

^b NATIONAL CENTER FOR AGRICULTURAL UTILIZATION RESEARCH   (United States)

^c WESTERN REGIONAL RESEARCH CENTER   (United States)

Author keywords

D Xylosidase; Bioenergy; Glycoside hydrolase; Protein engineering; Selection

Indexed keywords

ACTIVE CATALYST; ACTIVE SITE; BIO-ENERGY; BIO-ETHANOL PRODUCTION; D-GLUCOSE; D-XYLOSE; ENZYME LIBRARIES; ENZYME PERFORMANCE; ERROR PRONE PCR; FOUR AMINO ACIDS; GLYCOSIDE HYDROLASES; HIGH-THROUGHPUT; PROTEIN ENGINEERING; SELENOMONAS; SIDE CHAINS; WILD TYPES; XYLOOLIGOSACCHARIDES; XYLOSIDASE;

AMINO ACIDS; BIOCHEMICAL ENGINEERING; BIOETHANOL; ENZYMES; ETHANOL; GENETIC ENGINEERING; GLUCOSE; ORGANIC ACIDS; SACCHARIFICATION;

XYLOSE;

AMINO ACID; BETA DEXTRO XYLOSIDASE; ENZYME INHIBITOR; MONOSACCHARIDE; UNCLASSIFIED DRUG; XYLAN 1,4 BETA XYLOSIDASE;

BIOCHEMISTRY; BIOENERGY; BIOENGINEERING; BIOFUEL; CATALYSIS; ENZYME ACTIVITY; HYDROLYSIS; PROTEIN;

ARTICLE; ENZYME ACTIVE SITE; HIGH THROUGHPUT SCREENING; LIBRARY; MUTATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PROTEIN ENGINEERING; WILD TYPE;

AMINO ACID SUBSTITUTION; CATALYTIC DOMAIN; ENZYME INHIBITORS; GLUCOSE; KINETICS; MUTAGENESIS; MUTATION, MISSENSE; OLIGOSACCHARIDES; POLYMERASE CHAIN REACTION; RECOMBINANT PROTEINS; SELENOMONAS; XYLOSE; XYLOSIDASES;

SELENOMONAS RUMINANTIUM;

EID: 77950630377     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-009-2335-7     Document Type: Article

References (27)

1. Aharoni A, Griffiths AD, Tawfik DS (2005) High-throughput screens and selections of enzyme-encoding genes. Curr Opin Chem Biol 9:210-216 (Pubitemid 40462492)
2. Bloom JD, Silberg JJ, Wilke CO, Drummond DA, Adami C, Arnold FH (2005) Thermodynamic prediction of protein neutrality. Proc Natl Acad Sci 102:606-611 (Pubitemid 40282712)
3. Brunzelle JS, Jordan DB, McCaslin DR, Olczak A, Wawrzak Z (2008) Structure of the two-subsite β-D-xylosidase from Selenomonas ruminantium in complex with 1, 3-bis[tris(hydroxymethyl)methylamino] propane. Arch Biochem Biophys 474:157-166
4. Brüx C, Ben-David A, Shallom-Shezifi D, Leon M, Niefind K, Shoham G, Shoham Y, Schomburg D (2006) The structure of an inverting GH43 β-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues. J Mol Biol 359:97-109
5. Chockalingam K, Luba J, Nick HS, Silverman DN, Zhao H (2006) Engineering and characterization of human manganese superoxide dismutase mutants with high activity and low product inhibition. FEBS J 273:4853-4861 (Pubitemid 44583510)
6. Daughterty PS, Chen G, Iverson BL, Georgiou G (2000) Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc Natl Acad Sci 97:2029-2034
7. Drummond DA, Iverson BL, Georgiou G, Arnold FH (2005) Why high-error-rate random mutagenesis libraries are enriched in functional and improved proteins. J Mol Biol 350:806-816
8. Durette PL, Horton D (1971) Conformational analysis of sugars and their derivatives. Adv Carbohydr Chem Biochem 26:49-125
9. Gill SC, von Hippel PH (1989) Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem 182:319-326
10. Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280:309-316
11. Jordan DB (2008) β-D-Xylosidase from Selenomonas ruminantium: catalyzed reactions with natural and artificial substrates. Appl Biochem Biotechnol 146:137-149
12. Jordan DB, Braker JD (2007) Inhibition of the two-subsite β-D-xylosidase from Selenomonas ruminantium by sugars: competitive, noncompetitive, double binding, and slow binding modes. Arch Biochem Biophys 465:231-246
13. Jordan DB, Li X-L (2007) Variation in relative substrate specificity of bifunctional β-D-xylosidase/α-L-arabinofuranosidase by singlesite mutations: roles of substrate distortion and recognition. Biochim Biophys Acta 1774:1192-1198
14. Jordan DB, Dien BS, Li X-L, Cotta, MA (2006) Hemicellulases for mediating biomass saccharification. In: Proceedings of Renewable Energy 2006, Makuhari Messe, Japan, pp. 1036-1041
15. Jordan DB, Li X-L, Dunlap CA, Whitehead TR, Cotta MA (2007a) β-D-Xylosidase from Selenomonas ruminantium of glycoside hydrolase family 43. Appl Biochem Biotechnol 136-140:93-104
16. Jordan DB, Li X-L, Dunlap CA, Whitehead TR, Cotta MA (2007b) Structure-function relationships of a catalytically efficient β-D-xylosidase. Appl Biochem Biotechnol 141:51-76
17. Jordan DB, Mertens JA, Braker JD (2009) Amino alcohols as probes of the two-subsite active site of β-D-xylosidase from Selenomonas ruminantium. Biochim Biophys Acta 1794:144-158
18. Kim MS, Lei XG (2008) Enhancing thermostability of Escherichia coli phytase App A2 by error-prone PCR. Appl Microbiol Biotechnol 79:69-75
19. Leatherbarrow RJ (2001) Grafit version 5. Erithacus Software Ltd., Horley
20. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25:1605-1612
21. Rothman SC, Voorhies M, Kirsch JF (2004) Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase. Protein Sci 13:763-772
22. Van Doorslaer E, Kersters-Hilderson H, De Bruyne CK (1985) Hydrolysis of β-D-xylo-oligosaccharides by β-D-xylosidase from Bacillus pumilus. Carbohydr Res 140:342-346
23. Wagschal K, Heng C, Lee CC, Robertson GH, Orts WJ, Wong DWS (2009) Purification and characterization of a glycoside hydrolase family 43 β-xylosidase from Geobacillus thermoleovorans IT-08. Appl Biochem Biotech 155:304-313
24. Whitehead TR, Cotta MA (2001) Identification of a broad-specificity xylosidase/arabinosidase important for xylooligosaccharide fermentation by the ruminal anaerobe Selenomonas ruminantium GA192. Curr Microbiol 43:293-298
25. Wiseman T, Williston S, Brandts JF, Lin L-N (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal Biochem 179:131-137
26. Yuan L, Kurek I, English J, Keenan R (2005) Laboratory-directed protein evolution. Microbiol Mol Biol Rev 69:373-392
27. Yun H, Hwang B-Y, Lee J-H, Kim B-G (2005) Use of enrichment culture for directed evolution of the Vibrio fluvialis JS17 ω-transaminase, which is resistant to product inhibition by aliphatic ketones. Appl Environ Microbiol 71:4220-4224