Industrial Enzymes Industrial Enzymes Structure, Function and Applications Edited by Julio Polaina and Andrew P. MacCabe Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Valencia, Spain AC.I.P.CataloguerecordforthisbookisavailablefromtheLibraryofCongress. ISBN978-1-4020-5376-4(HB) ISBN978-1-4020-5377-1(e-book) PublishedbySpringer, P.O.Box17,3300AADordrecht,TheNetherlands. www.springer.com Coverillustration:CrystalstructureofxylanaseBfromBacillussp.BP-23. CourtesyofJuliaSanz-Aparicio. Printedonacid-freepaper AllRightsReserved ©2007Springer Nopartofthisworkmaybereproduced,storedinaretrievalsystem,ortransmitted inanyformorbyanymeans,electronic,mechanical,photocopying,microfilming,recording orotherwise,withoutwrittenpermissionfromthePublisher,withtheexception ofanymaterialsuppliedspecificallyforthepurposeofbeingentered andexecutedonacomputersystem,forexclusiveusebythepurchaserofthework. CONTENTS Preface. Industrial Enzymes in the 21st Century ix Julio Polaina and Andrew P. MacCabe Contributors xi SECTION A. CARBOHYDRATE ACTIVE ENZYMES Chapter 1. Amylolytic Enzymes: Types, Structures and Specificities 3 Martin Machovicˇ and Štefan Janecˇek Chapter 2. The Use of Starch Processing Enzymes in the Food Industry 19 Józef Synowiecki Chapter 3. Cellulases for Biomass Conversion 35 QiXu,WilliamS.Adney,Shi-YouDingandMichaelE.Himmel Chapter 4. Cellulases in the Textile Industry 51 Arja Miettinen-Oinonen Chapter 5. Xylanases: Molecular Properties and Applications 65 F. I. Javier Pastor, Óscar Gallardo, Julia Sanz-Aparicio and Pilar Díaz Chapter 6. Microbial Xylanolytic Carbohydrate Esterases 83 Evangelos Topakas and Paul Christakopoulos Chapter 7. Structural and Biochemical Properties of Pectinases 99 Sathyanarayana N. Gummadi, N. Manoj and D. Sunil Kumar Chapter 8. (cid:2)-L-rhamnosidases: Old and New Insights 117 Paloma Manzanares, Salvador Vallés, Daniel Ramón and Margarita Orejas v vi CONTENTS Chapter 9. Application of Glycosidases and Transglycosidases in the Synthesis of Oligosaccharides 141 Francisco J. Plou, Aránzazu Gómez de Segura and Antonio Ballesteros SECTION B. PEPTIDASES Chapter10. An Introduction to Peptidases and the MEROPS Database 161 Neil D. Rawlings, Fraser R. Morton and Alan J. Barrett Chapter11. Cysteine Proteases 181 Zbigniew Grzonka, Franciszek Kasprzykowski and Wiesław Wiczk Chapter12. Subtilisin 197 John Donlon Chapter13. Aspartic Proteases Used in Cheese Making 207 FélixClaverie-Martín and María C. Vega-Hernández Chapter14. Metalloproteases 221 Johanna Mansfeld Chapter15. Aminopeptidases 243 Yolanda Sanz SECTION C. LIPASES Chapter16. Lipases: Molecular Structure and Function 263 Marina Lotti and Lilia Alberghina Chapter17. Use of Lipases in the Industrial Production of Esters 283 Soundar Divakar and Balaraman Manohar Chapter18. Use of Lipases in Organic Synthesis 301 Vicente Gotor-Fernández and Vicente Gotor Chapter19. Use of Lipases for the Production of Biodiesel 317 Andrea Salis, Maura Monduzzi and Vincenzo Solinas CONTENTS vii Chapter20. Use of Lipases in the Synthesis of Structured Lipids in Supercritical Carbon Dioxide 341 José da Cruz Francisco, Simon P. Gough and Estera S. Dey SECTION D. NUCLEIC ACIDS ENZYMES Chapter21. Restriction and Homing Endonucleases 357 Krzysztof J. Skowronek and Janusz M. Bujnicki Chapter22. DNA Polymerases for PCR Applications 379 Régen Drouin, Walid Dridi and Oumar Samassekou Chapter23. Prokaryotic Reverse Transcriptases 403 Bert C. Lampson Chapter24. Dicer: Structure, Function and Role in RNA-Dependent Gene-Silencing Pathways 421 Justin M. Pare and Tom C. Hobman SECTION E. OXIDOREDUCTASES AND OTHER ENZYMES OF DIVERSE FUNCTION Chapter25. Hydrogen Peroxide Producing and Decomposing Enzymes: Their Use in Biosensors and Other Applications 441 Nóra Adányi, Teréz Barna, Tamás Emri, Márton Miskei and István Pócsi Chapter26. Laccases: Biological Functions, Molecular Structure and Industrial Applications 461 Miguel Alcalde Chapter27. High Redox Potential Peroxidases 477 Ángel T. Martínez Chapter28. Amino Acid Dehydrogenases 489 Stephen Y.K. Seah Chapter29. Phytase: Source, Structure and Application 505 Xin Gen Lei, Jesus M. Porres, Edward J. Mullaney and Henrik Brinch-Pedersen viii CONTENTS Chapter30. Nitrile Hydrolases 531 Praveen Kaul, Anirban Banerjee and Uttam Chand Banerjee Chapter31. Aspartases: Molecular Structure, Biochemical Function and Biotechnological Applications 549 Tomohiro Mizobata and Yasushi Kawata Chapter32. Transglutaminases 567 María Jesús Arrizubieta Chapter33. Penicillin Acylases 583 David W. Spence and Martin Ramsden Chapter34. Hydantoinases 599 Yun-Peng Chao, Chung-Jen Chiang, Jong-Tzer Chern and Jason T.C. Tzen SubjectIndex 607 OrganismIndex 637 PREFACE INDUSTRIAL ENZYMES IN THE 21st CENTURY Man’s use of enzymes dates back to the earliest times of civilization. Important human activities in primitive communities such as the production of certain types of foods and beverages, and the tanning of hides and skins to produce leather for garments, involved the application of enzyme activities, albeit unknowingly. However, not until the 19th century with the development of biochemistry and the pioneering work of a number of eminent scientists did the nature of enzymes and how they work begin to be clarified. In France Anselme Payen and Jean-François Persoz described the isolation of an amylolytic substance from germinating barley (1833).ShortlyafterwardstheSwedishchemistJönsJacobBerzeliuscoinedtheterm catalysis(1835)todescribethepropertyofcertainsubstancestoacceleratechemical reactions. In Germany the physiologist Theodor Schwann discovered the digestive enzyme pepsin (1836), Wilhelm Kühne proposed the term ‘enzyme’ (1877), and the brothers Hans and Eduard Buchner demonstrated that the transformation of glucoseintoethanolcouldbecarriedoutbychemicalsubstances(enzymes)present in cell-free extracts of yeast (1897). In the 1870’s the Danish chemist Christian Hansensucceededinobtainingpurerennetfromcalves’stomachs,theuseofwhich in cheese-making resulted in considerable improvements in both product quantity andquality.Shortlythereafterheindustrialisedtheproductionofrennetthussetting in motion the first enzyme production industry. During the 20th century the recognition that enzymes are proteins along with the design of techniques for their purification and analysis, principally the work of JamesB.SumnerandKajLinderstrøm-Lang,pavedthewayforthedevelopmentof procedures for their industrial production and use. The nineteen-sixties witnessed two major breakthroughs that had a major impact on the enzyme industry: the commercialisationofglucoamylasewhichcatalysestheproductionofglucosefrom starch with much greater efficiency than that of the chemical procedure of acid hydrolysis, and the launch of the first enzyme-containing detergents. The devel- opment of genetic engineering in the eighties provided the tools necessary for the productionandcommercialisationofnewenzymesthusseedingasecondexplosive expansion to the current billion dollar enzyme industry. Recent advances in X-ray crystallographyandotheranalyticalmethodsinthefieldofproteinchemistryalong withtheeverincreasingamountsofbiologicalinformationavailablefromgenomics ix x PREFACE programsandmoleculartechniquessuchasdirectedevolutionandgeneandgenome shuffling, are bringing powerful means to bear on the study and manipulation of enzyme structure and function. The search for improvements in existing enzyme- catalysed procedures, the need to develop new technologies and the increasing concernforresponsibleuseandreuseofrawmaterialscanbeexpectedtostimulate not only the rational modification of enzymes to match specific requirements but also the design of new enzymes with totally novel properties. The aim of this book is to provide in a single volume an updated revision of the most important types of industrial enzymes based on consideration of their physicochemicalandcatalyticproperties,three-dimensionalstructure,andtherange ofcurrentandforeseeableapplications.Thefirstsectionofthisvolumeisdedicated to the carbohydrate active enzymes which are extensively used not only in many food industry applications (baking, beverage production, starch processing, etc.) but also in the industrial production of textiles, detergents, paper, ethanol, etc. The second section, on peptidases, begins with an introductory chapter about the MEROPSdatabasewhichconstitutesthecurrentclassificationofreferenceforthis important group of enzymes, and subsequent chapters review the most industrially relevant types of peptidases. The section on lipases places special emphasis on the increasing application of these enzymes in synthetic processes. Nucleic acid modifying activities are considered in the fourth section. Whilst the nature of the applications and scale of use of the latter are not yet comparable to those of the enzymes considered in the preceding sections, they are of growing in importance given the indispensability of some in highly specialised fields including basic and applied research, medicine, pharmaceuticals, agronomy and forensics. The final sectionconsidersanumberofimportantenzymesthatcannotbeclassifiedintoany of the other sections. Wewishtothankeveryoneinvolvedinmakingthisbookpossibleandhopethat it will become a tool equally useful to researchers, industrialists and students. Julio Polaina Andrew P. MacCabe CONTRIBUTORS Adányi, Nóra, sect. E, ch. 25, p. 439 Adney, William S., sect. A, ch. 3, p. 35 Alberghina, Lilia, sect. C, ch. 16, p. 263 Alcalde, Miguel, sect. E, ch. 26, p. 459 Arrizubieta, María J., sect. E, ch. 32, p. 565 Ballesteros, Antonio, sect. A, ch. 9, p. 141 Banerjee, Anirban, sect. E, ch. 30, p. 529 Banerjee, Uttam Chand, sect. E, ch. 30, p. 529 Barna, Teréz, sect. E, ch. 25, p. 439 Barrett, Alan J., sect. B, ch. 10, p. 161 Brinch-Pedersen, Henrik, sect. E, ch. 29, p. 503 Bujnicki, Janusz M., sect. D, ch. 21, p. 355 Chao, Yun-Peng, sect. E, ch. 34, p. 597 Chern, Jong-Tzer, sect. E, ch. 34, p. 597 Chiang, Chung-Jen, sect. E, ch. 34, p. 597 Christakopoulos, Paul, sect. A, ch. 6, p. 83 Claveríe-Martín, Félix, sect. B, ch. 13, p. 207 Dey, Estera S., sect. C, ch. 20, p. 339 Díaz, Pilar, sect. A, ch. 5. p. 65 Ding, Shi-You, sect. A, ch, 3, p. 35 Divakar, Soundar, sect. C, ch. 17, p. 283 Donlon, John, sect. B, ch. 12, p. 197 Dridi, Walid, sect. D, ch. 22, p. 377 Drouin, Régen, sect. D, ch. 22, p. 377 Emri, Tamás, sect. E, ch. 25, p. 439 Francisco, José da Cruz, sect. C, ch. 20, p. 339 Gallardo, Óscar, sect. A, ch. 5, p. 65 Gómez de Segura, Aránzazu, sect. A, ch. 9, p. 141 Gotor, Vicente, sect. C, ch. 18, p. 301 Gotor-Fernández, Vicente, sect. C, ch. 18, p. 301 Gough, Simon P., sect. C, ch. 20, p. 339 Grzonka, Zbigniew, sect. B, ch. 11, p. 181 Gummadi, Sathyanarayana N., sect. A, ch. 7, p. 99 Himmel, Michael E., sect. A, ch. 3, p. 35 xi