Crystal structure of a feruloyl esterase belonging to the tannase family: A disulfide bond near a catalytic triad
Kentaro Suzuki
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorAkane Hori
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorKazusa Kawamoto
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorRatna Rajesh Thangudu
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland
Search for more papers by this authorTakuya Ishida
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorKiyohiko Igarashi
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorMasahiro Samejima
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorChihaya Yamada
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakatoshi Arakawa
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakayoshi Wakagi
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakuya Koseki
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorCorresponding Author
Shinya Fushinobu
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Correspondence to: Shinya Fushinobu, Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. E-mail: [email protected]Search for more papers by this authorKentaro Suzuki
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorAkane Hori
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorKazusa Kawamoto
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorRatna Rajesh Thangudu
National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland
Search for more papers by this authorTakuya Ishida
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorKiyohiko Igarashi
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorMasahiro Samejima
Department of Biomaterial Sciences, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorChihaya Yamada
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakatoshi Arakawa
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakayoshi Wakagi
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Search for more papers by this authorTakuya Koseki
Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
Search for more papers by this authorCorresponding Author
Shinya Fushinobu
Department of Biotechnology, The University of Tokyo, Tokyo, Japan
Correspondence to: Shinya Fushinobu, Department of Biotechnology, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. E-mail: [email protected]Search for more papers by this authorABSTRACT
Feruloyl esterase (FAE) catalyzes the hydrolysis of the ferulic and diferulic acids present in plant cell wall polysaccharides, and tannase catalyzes the hydrolysis of tannins to release gallic acid. The fungal tannase family in the ESTHER database contains various enzymes, including FAEs and tannases. Despite the importance of FAEs and tannases in bioindustrial applications, three-dimensional structures of the fungal tannase family members have been unknown. Here, we determined the crystal structure of FAE B from Aspergillus oryzae (AoFaeB), which belongs to the fungal tannase family, at 1.5 Å resolution. AoFaeB consists of a catalytic α/β-hydrolase fold domain and a large lid domain, and the latter has a novel fold. To estimate probable binding models of substrates in AoFaeB, an automated docking analysis was performed. In the active site pocket of AoFaeB, residues responsible for the substrate specificity of the FAE activity were identified. The catalytic triad of AoFaeB comprises Ser203, Asp417, and His457, and the serine and histidine residues are directly connected by a disulfide bond of the neighboring cysteine residues, Cys202 and Cys458. This structural feature, the “CS-D-HC motif,” is unprecedented in serine hydrolases. A mutational analysis indicated that the novel structural motif plays essential roles in the function of the active site. Proteins 2014; 82:2857–2867. © 2014 Wiley Periodicals, Inc.
Supporting Information
Additional Supporting Information may be found in the online version of this article.
Filename | Description |
---|---|
prot24649-sup-0001-suppinfo01.pdf1 MB |
Supplementary Information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
REFERENCES
- 1 Benoit I, Danchin EG, Bleichrodt RJ, de Vries RP. Biotechnological applications and potential of fungal feruloyl esterases based on prevalence, classification and biochemical diversity. Biotechnol Lett 2008; 30: 387–396.
- 2 Koseki T, Fushinobu S, Ardiansyah, Shirakawa H, Komai M. Occurrence, properties, and applications of feruloyl esterases. Appl Microbiol Biotechnol 2009; 84: 803–810.
- 3 Faulds CB. What can feruloyl esterases do for us? Phytochem Rev 2010; 9: 121–132.
- 4 Crepin VF, Faulds CB, Connerton IF. Functional classification of the microbial feruloyl esterases. Appl Microbiol Biotechnol 2004; 63: 647–652.
- 5 Nardini M, Dijkstra BW. Alpha/beta hydrolase fold enzymes: the family keeps growing. Curr Opin Struct Biol 1999; 9: 732–737.
- 6 Lenfant N, Hotelier T, Velluet E, Bourne Y, Marchot P, Chatonnet A. ESTHER, the database of the alpha/beta-hydrolase fold superfamily of proteins: tools to explore diversity of functions. Nucleic Acids Res 2013; 41: D423–D429.
- 7 Hermoso JA, Sanz-Aparicio J, Molina R, Juge N, Gonzalez R, Faulds CB. The crystal structure of feruloyl esterase A from Aspergillus niger suggests evolutive functional convergence in feruloyl esterase family. J Mol Biol 2004; 338: 495–506.
- 8 Prates JA, Tarbouriech N, Charnock SJ, Fontes CM, Ferreira LM, Davies GJ. The structure of the feruloyl esterase module of xylanase 10B from Clostridium thermocellum provides insights into substrate recognition. Structure 2001; 9: 1183–1190.
- 9 Goldstone DC, Villas-Boas SG, Till M, Kelly WJ, Attwood GT, Arcus VL. Structural and functional characterization of a promiscuous feruloyl esterase (Est1E) from the rumen bacterium Butyrivibrio proteoclasticus. Proteins 2010; 78: 1457–1469.
- 10 de Vries RP, vanKuyk PA, Kester HC, Visser J. The Aspergillus niger faeB gene encodes a second feruloyl esterase involved in pectin and xylan degradation and is specifically induced in the presence of aromatic compounds. Biochem J 2002; 363: 377–386.
- 11 Garcia-Conesa MT, Crepin VF, Goldson AJ, Williamson G, Cummings NJ, Connerton IF, Faulds CB, Kroon PA. The feruloyl esterase system of Talaromyces stipitatus: production of three discrete feruloyl esterases, including a novel enzyme, TsFaeC, with a broad substrate specificity. J Biotechnol 2004; 108: 227–241.
- 12 Shin HD, Chen RR. A type B feruloyl esterase from Aspergillus nidulans with broad pH applicability. Appl Microbiol Biotechnol 2007; 73: 1323–1330.
- 13 Moukouli M, Topakas E, Christakopoulos P. Cloning, characterization and functional expression of an alkalitolerant type C feruloyl esterase from Fusarium oxysporum. Appl Microbiol Biotechnol 2008; 79: 245–254.
- 14 Koseki T, Hori A, Seki S, Murayama T, Shiono Y. Characterization of two distinct feruloyl esterases, AoFaeB and AoFaeC, from Aspergillus oryzae. Appl Microbiol Biotechnol 2009; 83: 689–696.
- 15 Yao J, Chen QL, Shen AX, Cao W, Liu YH. A novel feruloyl esterase from a soil metagenomic library with tannase activity. J Mol Catal B Enzymatic 2013; 95: 55–61.
- 16 Hatamoto O, Watarai T, Kikuchi M, Mizusawa K, Sekine H. Cloning and sequencing of the gene encoding tannase and a structural study of the tannase subunit from Aspergillus oryzae. Gene 1996; 175: 215–221.
- 17 Koseki T, Mihara K, Murayama T, Shiono Y. A novel Aspergillus oryzae esterase that hydrolyzes 4-hydroxybenzoic acid esters. FEBS Lett 2010; 584: 4032–4036.
- 18 Koseki T, Asai S, Saito N, Mori M, Sakaguchi Y, Ikeda K, Shiono Y. Characterization of a novel lipolytic enzyme from Aspergillus oryzae. Appl Microbiol Biotechnol 2013; 97: 5351–5357.
- 19 Lekha PK, Lonsane BK. Production and application of tannin acyl hydrolase: state of the art. Adv Appl Microbiol 1997; 44: 215–260.
- 20 Ren B, Wu M, Wang Q, Peng X, Wen H, McKinstry WJ, Chen Q. Crystal structure of tannase from Lactobacillus plantarum. J Mol Biol 2013; 425: 2737–2751.
- 21 Matoba Y, Tanaka N, Noda M, Higashikawa F, Kumagai T, Sugiyama M. Crystallographic and mutational analyses of tannase from Lactobacillus plantarum. Proteins 2013; 81: 2052–2058.
- 22 Banerjee A, Jana A, Pati BR, Mondal KC, Das Mohapatra PK. Characterization of tannase protein sequences of bacteria and fungi: an in silico study. Protein J 2012; 31: 306–327.
- 23 Aguilar CN, Rodriguez R, Gutierrez-Sanchez G, Augur C, Favela-Torres E, Prado-Barragan LA, Ramirez-Coronel A, Contreras-Esquivel JC. Microbial tannases: advances and perspectives. Appl Microbiol Biotechnol 2007; 76: 47–59.
- 24 Kumar CS, Subramanian R, Rao LJ. Application of enzymes in the production of RTD black tea beverages: a review. Crit Rev Food Sci Nutr 2013; 53: 180–197.
- 25 Machida M, Yamada O, Gomi K. Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future. DNA Res 2008; 15: 173–183.
- 26 Igarashi K, Ishida T, Hori C, Samejima M. Characterization of an endoglucanase belonging to a new subfamily of glycoside hydrolase family 45 of the basidiomycete Phanerochaete chrysosporium. Appl Environ Microbiol 2008; 74: 5628–5634.
- 27 Miyatake H, Hasegawa T, Yamano A. New methods to prepare iodinated derivatives by vaporizing iodine labelling (VIL) and hydrogen peroxide VIL (HYPER-VIL). Acta Crystallogr D Biol Crystallogr 2006; 62: 280–289.
- 28 Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1997; 276: 307–326.
- 29 Rappleye J, Innus M, Weeks CM, Miller R. SnB version 2.2: an example of crystallographic multiprocessing. J Appl Crystallogr 2002; 35: 374–376.
- 30 Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999; 55: 849–861.
- 31 Perrakis A, Morris R, Lamzin VS. Automated protein model building combined with iterative structure refinement. Nat Struct Biol 1999; 6: 458–463.
- 32 Emsley P, Lohkamp B, Scott WG, Cowtan K. Features and development of Coot. Acta Crystallogr D Biol Crystallogr 2010; 66: 486–501.
- 33 Murshudov GN, Vagin AA, Dodson EJ. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 1997; 53: 240–255.
- 34 Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 2010; 31: 455–461.
- 35 Krissinel E, Henrick K. Inference of macromolecular assemblies from crystalline state. J Mol Biol 2007; 372: 774–797.
- 36 Botos I, Wlodawer A. The expanding diversity of serine hydrolases. Curr Opin Struct Biol 2007; 17: 683–690.
- 37 McAuley KE, Svendsen A, Patkar SA, Wilson KS. Structure of a feruloyl esterase from Aspergillus niger. Acta Crystallogr D Biol Crystallogr 2004; 60: 878–887.
- 38 Crepin VF, Faulds CB, Connerton IF. Production and characterization of the Talaromyces stipitatus feruloyl esterase FAEC in Pichia pastoris: identification of the nucleophilic serine. Protein Expr Purif 2003; 29: 176–184.
- 39 Sakamoto T, Nishimura S, Kato T, Sunagawa Y, Tsuchiyama M, Kawasaki H. Efficient extraction of ferulic acid from sugar beet pulp using the culture supernatant of Penicillium chrysogenum. J Appl Glycosci 2005; 52: 115–120.
- 40 Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995; 247: 536–540.
- 41 Gandhimathi A, Nair AG, Sowdhamini R. PASS2 version 4: an update to the database of structure-based sequence alignments of structural domain superfamilies. Nucleic Acids Res 2012; 40: D531–534.
- 42 Thangudu RR, Manoharan M, Srinivasan N, Cadet F, Sowdhamini R, Offmann B. Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families. BMC Struct Biol 2008; 8: 55.
- 43 Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Jackson JD, Ke Z, Lanczycki CJ, Lu F, Marchler GH, Mullokandov M, Omelchenko MV, Robertson CL, Song JS, Thanki N, Yamashita RA, Zhang D, Zhang N, Zheng C, Bryant SH. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res 2011; 39: D225–D229.
- 44 Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011; 39: W29–W37.
- 45 Schuster-Bockler B, Schultz J, Rahmann S. HMM Logos for visualization of protein families. BMC Bioinformatics 2004; 5: 7.
- 46 Martinez C, De Geus P, Lauwereys M, Matthyssens G, Cambillau C. Fusarium solani cutinase is a lipolytic enzyme with a catalytic serine accessible to solvent. Nature 1992; 356: 615–618.
- 47 Liu Z, Gosser Y, Baker PJ, Ravee Y, Lu Z, Alemu G, Li H, Butterfoss GL, Kong XP, Gross R, Montclare JK. Structural and functional studies of Aspergillus oryzae cutinase: enhanced thermostability and hydrolytic activity of synthetic ester and polyester degradation. J Am Chem Soc 2009; 131: 15711–15716.
- 48 Matak MY, Moghaddam ME. The role of short-range Cys171-Cys178 disulfide bond in maintaining cutinase active site integrity: a molecular dynamics simulation. Biochem Biophys Res Commun 2009; 390: 201–204.