51
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Najmudin S, Pinheiro BA, Romão MJ, Prates JAM, Fontes CMGA. Purification, crystallization and crystallographic analysis of Clostridium thermocellum endo-1,4-beta-D-xylanase 10B in complex with xylohexaose. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:715-8. [PMID: 18678939 PMCID: PMC2494957 DOI: 10.1107/s1744309108019696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2008] [Accepted: 06/27/2008] [Indexed: 11/10/2022]
Abstract
The cellulosome of Clostridium thermocellum is a highly organized multi-enzyme complex of cellulases and hemicellulases involved in the hydrolysis of plant cell-wall polysaccharides. The bifunctional multi-modular xylanase Xyn10B is one of the hemicellulase components of the C. thermocellum cellulosome. The enzyme contains an internal glycoside hydrolase family 10 catalytic domain (GH10) and a C-terminal family 1 carbohydrate esterase domain (CE1). The N-terminal moiety of Xyn10B (residues 32-551), comprising a carbohydrate-binding module (CBM22-1) and the GH10 E337A mutant, was crystallized in complex with xylohexaose. The crystals belong to the trigonal space group P3(2)21 and contain a dimer in the asymmetric unit. The crystals diffracted to beyond 2.0 A resolution.
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Affiliation(s)
- Shabir Najmudin
- REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
| | - Benedita A. Pinheiro
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Maria J. Romão
- REQUIMTE, Departamento de Química, FCT-UNL, 2829-516 Caparica, Portugal
| | - José A. M. Prates
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Carlos M. G. A. Fontes
- CIISA – Faculdade de Medicina Veterinária, Universidade Técnica de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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52
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Fazary AE, Ju YH. Feruloyl esterases as biotechnological tools: current and future perspectives. Acta Biochim Biophys Sin (Shanghai) 2007; 39:811-28. [PMID: 17989872 DOI: 10.1111/j.1745-7270.2007.00348.x] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Feruloyl esterases represent a diverse group of hydrolases catalyzing the cleavage and formation of ester bonds between plant cell wall polysaccharide and phenolic acid. They are widely distributed in plants and microorganisms. Besides lipases, a considerable number of microbial feruloyl esterases have also been discovered and overexpressed. This review summarizes the latest research on their classification, production, and biophysicochemical properties. Special emphasis is given to the importance of that type of enzyme and their related phenolic ferulic acid compound in biotechnological processes, and industrial and medicinal applications.
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Affiliation(s)
- Ahmed E Fazary
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 106-07, Taiwan, China
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53
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54
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Palackal N, Lyon CS, Zaidi S, Luginbühl P, Dupree P, Goubet F, Macomber JL, Short JM, Hazlewood GP, Robertson DE, Steer BA. A multifunctional hybrid glycosyl hydrolase discovered in an uncultured microbial consortium from ruminant gut. Appl Microbiol Biotechnol 2007; 74:113-24. [PMID: 17103163 DOI: 10.1007/s00253-006-0645-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2006] [Revised: 08/16/2006] [Accepted: 08/22/2006] [Indexed: 10/23/2022]
Abstract
A unique multifunctional glycosyl hydrolase was discovered by screening an environmental DNA library prepared from a microbial consortium collected from cow rumen. The protein consists of two adjacent catalytic domains. Sequence analysis predicted that one domain conforms to glycosyl hydrolase family 5 and the other to family 26. The enzyme is active on several different beta-linked substrates and possesses mannanase, xylanase, and glucanase activities. Site-directed mutagenesis studies on the catalytic residues confirmed the presence of two functionally independent catalytic domains. Using site-specific mutations, it was shown that one catalytic site hydrolyzes beta-1,4-linked mannan substrates, while the second catalytic site hydrolyzes beta-1,4-linked xylan and beta-1,4-linked glucan substrates. Polysaccharide Analysis using Carbohydrate gel Electrophoresis (PACE) also confirmed that the enzyme has discrete domains for binding and hydrolysis of glucan- and mannan-linked polysaccharides. Such multifunctional enzymes have many potential industrial applications in plant processing, including biomass saccharification, animal feed nutritional enhancement, textile, and pulp and paper processing.
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Affiliation(s)
- Nisha Palackal
- Diversa Corporation, 4955 Directors Place, San Diego, CA 92121, USA
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55
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Pothiraj C, Kanmani P, Balaji P. Bioconversion of lignocellulose materials. MYCOBIOLOGY 2006; 34:159-65. [PMID: 24039492 PMCID: PMC3769567 DOI: 10.4489/myco.2006.34.4.159] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2006] [Indexed: 05/05/2023]
Abstract
One of the most economically viable processes for the bioconversion of many lignocellulosic waste is represented by white rot fungi. Phanerochaete chrysosporium is one of the important commercially cultivated fungi which exhibit varying abilities to utilize different lignocellulosic as growth substrate. Examination of the lignocellulolytic enzyme profiles of the two organisms Phanerochaete chrysosporium and Rhizopus stolonifer show this diversity to be reflected in qualitative variation in the major enzymatic determinants (ie cellulase, xylanase, ligninase and etc) required for substrate bioconversion. For example P. chrysosporium which is cultivated on highly lignified substrates such as wood (or) sawdust, produces two extracellular enzymes which have associated with lignin deploymerization. (Mn peroxidase and lignin peroxidase). Conversely Rhizopus stolonifer which prefers high cellulose and low lignin containg substrates produce a family of cellulolytic enzymes including at least cellobiohydrolases and β-glucosidases, but very low level of recognized lignin degrading enzymes.
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Affiliation(s)
- C Pothiraj
- Department of Microbiology, VHNSN College 626001, Tamilnadu, S. India
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56
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Vafiadi C, Topakas E, Christakopoulos P, Faulds CB. The feruloyl esterase system of Talaromyces stipitatus: Determining the hydrolytic and synthetic specificity of TsFaeC. J Biotechnol 2006; 125:210-21. [PMID: 16584797 DOI: 10.1016/j.jbiotec.2006.02.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 02/02/2006] [Accepted: 02/17/2006] [Indexed: 10/24/2022]
Abstract
The active site of the recombinant Talaromyces stipitatus type-C feruloyl esterase (TsFaeC) was probed using a series of C1-C4 alkyl ferulates and methyl esters of phenylalkanoic and cinnamic acids. The enzyme was active on 23 of the 34 substrates tested. Lengthening or shortening the aliphatic side chain while maintaining the same aromatic substitutions completely abolished the enzyme activity. Maintaining the phenylpropenoate structure but altering the substitutions of the aromatic ring demonstrated the importance of hydroxyl groups on meta and/or para position of the benzoic ring. The highest catalytic efficiency of TsFaeC for methyl cinnamates was shown on methyl 3,4-dihydroxy cinnamate and on its hydro form (3,4-dihydroxy-phenyl-propionate). Maintaining the ferulate structure but altering the esterified alkyl group, the comparison of k(cat) and k(cat)/K(m) values showed that the enzyme hydrolysed faster and more efficiently than ethyl ferulate. Alkyl ferulates were applied also for substrate selectivity mapping of feruloyl esterase to catalyze feruloyl group transfer to l-arabinose, using as a reaction system a ternary water-organic mixture consisting of n-hexane, t-butanol and water. The reaction parameters affecting the feruloylation rate and the conversion of the enzymatic synthesis, such as the composition of the reaction media, temperature, substrate and enzyme concentration have been investigated.
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Affiliation(s)
- Christina Vafiadi
- Biotechnology Laboratory, Chemical Engineering Department, National Technical University of Athens, 5 Iroon Polytechniou Str, Zografou Campus, 15700 Athens, Greece
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57
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Barooah N, Sarma RJ, Batsanov AS, Baruah JB. Structural aspects of adducts of N-phthaloylglycine and its derivatives. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2006.01.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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58
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Taylor EJ, Gloster TM, Turkenburg JP, Vincent F, Brzozowski AM, Dupont C, Shareck F, Centeno MSJ, Prates JAM, Puchart V, Ferreira LMA, Fontes CMGA, Biely P, Davies GJ. Structure and Activity of Two Metal Ion-dependent Acetylxylan Esterases Involved in Plant Cell Wall Degradation Reveals a Close Similarity to Peptidoglycan Deacetylases. J Biol Chem 2006; 281:10968-75. [PMID: 16431911 DOI: 10.1074/jbc.m513066200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzymatic degradation of plant cell wall xylan requires the concerted action of a diverse enzymatic syndicate. Among these enzymes are xylan esterases, which hydrolyze the O-acetyl substituents, primarily at the O-2 position of the xylan backbone. All acetylxylan esterase structures described previously display a alpha/beta hydrolase fold with a "Ser-His-Asp" catalytic triad. Here we report the structures of two distinct acetylxylan esterases, those from Streptomyces lividans and Clostridium thermocellum, in native and complex forms, with x-ray data to between 1.6 and 1.0 A resolution. We show, using a novel linked assay system with PNP-2-O-acetylxyloside and a beta-xylosidase, that the enzymes are sugar-specific and metal ion-dependent and possess a single metal center with a chemical preference for Co2+. Asp and His side chains complete the catalytic machinery. Different metal ion preferences for the two enzymes may reflect the surprising diversity with which the metal ion coordinates residues and ligands in the active center environment of the S. lividans and C. thermocellum enzymes. These "CE4" esterases involved in plant cell wall degradation are shown to be closely related to the de-N-acetylases involved in chitin and peptidoglycan degradation (Blair, D. E., Schuettelkopf, A. W., MacRae, J. I., and Aalten, D. M. (2005) Proc. Natl. Acad. Sci. U. S. A., 102, 15429-15434), which form the NodB deacetylase "superfamily."
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Affiliation(s)
- Edward J Taylor
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, United Kingdom
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59
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Puchart V, Gariépy MC, Shareck F, Dupont C. Identification of catalytically important amino acid residues of Streptomyces lividans acetylxylan esterase A from carbohydrate esterase family 4. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:263-74. [PMID: 16434244 DOI: 10.1016/j.bbapap.2005.11.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Revised: 11/05/2005] [Accepted: 11/21/2005] [Indexed: 11/16/2022]
Abstract
Multiple sequence alignment of Streptomyces lividans acetylxylan esterase A and other carbohydrate esterase family 4 enzymes revealed the following conserved amino acid residues: Asp-12, Asp-13, His-62, His-66, Asp-130, and His-155. These amino acids were mutated in order to investigate a functional role of these residues in catalysis. Replacement of the conserved histidine residues by alanine caused significant reduction of enzymatic activity. Maintenance of ionizable carboxylic group in side chains of amino acids at positions 12, 13, and 130 seems to be necessary for catalytic efficiency. The absence of conserved serine excludes a possibility that the enzyme is a serine esterase, in contrast to acetylxylan esterases of carbohydrate esterase families 1, 5, and 7. On the contrary, total conservation of Asp-12, Asp-13, Asp-130, and His-155 along with dramatic decrease in enzyme activity of mutants of either of these residues lead us to a suggestion that acetylxylan esterase A from Streptomyces lividans and, by inference, other members of carbohydrate esterase family 4 are aspartic deacetylases. We propose that one component of the aspartate dyad/triad functions as a catalytic nucleophile and the other one(s) as a catalytic acid/base. The ester/amide bond cleavage would proceed via a double displacement mechanism through covalently linked acetyl-enzyme intermediate of mixed anhydride type.
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Affiliation(s)
- Vladimír Puchart
- Institut National de la Recherche Scientifique-Institut Armand-Frappier, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7.
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60
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Faulds CB, Molina R, Gonzalez R, Husband F, Juge N, Sanz-Aparicio J, Hermoso JA. Probing the determinants of substrate specificity of a feruloyl esterase, AnFaeA, from Aspergillus niger. FEBS J 2005; 272:4362-71. [PMID: 16128806 DOI: 10.1111/j.1742-4658.2005.04849.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Feruloyl esterases hydrolyse phenolic groups involved in the cross-linking of arabinoxylan to other polymeric structures. This is important for opening the cell wall structure making material more accessible to glycoside hydrolases. Here we describe the crystal structure of inactive S133A mutant of type-A feruloyl esterase from Aspergillus niger (AnFaeA) in complex with a feruloylated trisaccharide substrate. Only the ferulic acid moiety of the substrate is visible in the electron density map, showing interactions through its OH and OCH(3) groups with the hydroxyl groups of Tyr80. The importance of aromatic and polar residues in the activity of AnFaeA was also evaluated using site-directed mutagenesis. Four mutant proteins were heterologously expressed in Pichia pastoris, and their kinetic properties determined against methyl esters of ferulic, sinapic, caffeic and p-coumaric acid. The k(cat) of Y80S, Y80V, W260S and W260V was drastically reduced compared to that of the wild-type enzyme. However, the replacement of Tyr80 and Trp260 with smaller residues broadened the substrate specificity of the enzyme, allowing the hydrolysis of methyl caffeate. The role of Tyr80 and Trp260 in AnFaeA are discussed in light of the three-dimensional structure.
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61
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Hatzakis NS, Smonou I. Asymmetric transesterification of secondary alcohols catalyzed by feruloyl esterase from Humicola insolens. Bioorg Chem 2005; 33:325-37. [PMID: 15970306 DOI: 10.1016/j.bioorg.2005.05.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 04/14/2005] [Accepted: 05/01/2005] [Indexed: 11/23/2022]
Abstract
A new asymmetric transesterification of secondary alcohols catalyzed by feruloyl esterase from Humicola insolens has been found. Although alcohols are not the natural substrates for this enzyme, a high R enantioselectivity was observed. Stereochemical studies showed that variations in substrate structure lead to strong variations in enantioselectivity. The highest enantioselectivities are obtained when the beta-carbon of the secondary alcohol is tertiary or quaternary.
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Affiliation(s)
- Nikos S Hatzakis
- Department of Chemistry, University of Crete, Iraklion 71409, Crete, Greece
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62
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Carvalho AL, Pires VMR, Gloster TM, Turkenburg JP, Prates JAM, Ferreira LMA, Romão MJ, Davies GJ, Fontes CMGA, Gilbert HJ. Insights into the structural determinants of cohesin-dockerin specificity revealed by the crystal structure of the type II cohesin from Clostridium thermocellum SdbA. J Mol Biol 2005; 349:909-15. [PMID: 15913653 DOI: 10.1016/j.jmb.2005.04.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2005] [Revised: 04/13/2005] [Accepted: 04/17/2005] [Indexed: 10/25/2022]
Abstract
The plant cell wall degrading enzymes expressed by anaerobic microorganisms form large multienzyme complexes (cellulosomes). Cellulosomes assemble by the Type I dockerins on the catalytic subunits binding to the reiterated Type I cohesins in the molecular scaffold, while Type II dockerin-cohesin interactions anchor the complex onto the bacterial cell surface. Type I and Type II cohesin, dockerin pairs show no cross-specificity. Here we report the crystal structure of the Type II cohesin (CohII) from the Clostridium thermocellum cell surface anchoring protein SdbA. The protein domain contains nine beta-strands and a small alpha-helix. The beta-strands assemble into two elongated beta-sheets that display a typical jelly roll fold. The structure of CohII is very similar to Type I cohesins, and the dockerin binding site, which is centred at beta-strands 3, 5 and 6, is likely to be conserved in the two proteins. Subtle differences in the topology of the binding sites and a lack of sequence identity in the beta-strands that comprise the core of the dockerin binding site explain why Type I and Type II cohesins display such distinct specificities for their target dockerins.
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Affiliation(s)
- Ana L Carvalho
- REQUIMTE/CQFB, Departamento de Química, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal
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63
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Dias FM, Goyal A, Gilbert HJ, Prates JA, Ferreira LM, Fontes CM. The N-terminal family 22 carbohydrate-binding module of xylanase 10B of Clostridium themocellumis not a thermostabilizing domain. FEMS Microbiol Lett 2004. [DOI: 10.1111/j.1574-6968.2004.tb09739.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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64
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Hermoso JA, Sanz-Aparicio J, Molina R, Juge N, González 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. [PMID: 15081808 DOI: 10.1016/j.jmb.2004.03.003] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2003] [Revised: 03/03/2004] [Accepted: 03/04/2004] [Indexed: 11/30/2022]
Abstract
As a component of the array of enzymes produced by micro-organisms to deconstruct plant cell walls, feruloyl esterases hydrolyze phenolic groups involved in the cross-linking of arabinoxylan to other polymeric structures. This is important for opening the cell wall structure, making material more accessible to glycosyl hydrolases. Here, we describe the first crystal structure of the non-modular type-A feruloyl esterase from Aspergillus niger (AnFaeA) solved at 2.5A resolution. AnFaeA displays an alpha/beta hydrolase fold similar to that found in fungal lipases and different from that reported for other feruloyl esterases. Crystallographic and site-directed mutagenesis studies allow us to identify the catalytic triad (Ser133-His247-Asp194) that forms the catalytic machinery of this enzyme. The active-site cavity is confined by a lid (residues 68-80), on the analogy of lipases, and by a loop (residues 226-244) that confers plasticity to the substrate-binding site. The lid presents a high ratio of polar residues, which in addition to a unique N-glycosylation site stabilises the lid in an open conformation, conferring the esterase character to this enzyme. A putative model for bound 5,5'-diferulic acid-linked arabinoxylan has been built, pointing to the more relevant residues involved in substrate recognition. Comparison with structurally related lipases reveals that subtle amino acid and conformational changes within a highly conserved protein fold may produce protein variants endowed with new enzymatic properties, while comparison with functionally related proteins points to a functional convergence after evolutionary divergence within the feruloyl esterases family.
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Affiliation(s)
- Juan A Hermoso
- Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto Química-Física Rocasolano C.S.I.C., Serrano 119, 28006 Madrid, Spain.
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65
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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; 108:227-41. [PMID: 15006424 DOI: 10.1016/j.jbiotec.2003.12.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2003] [Revised: 11/24/2003] [Accepted: 12/08/2003] [Indexed: 10/26/2022]
Abstract
Several extracellular feruloyl esterases were produced by the mesophilic fungus Talaromyces stipitatus when grown on selective carbon sources in liquid media. Type-A and Type-B feruloyl esterases, as defined by their substrate specificity against methyl hydroxycinnamates, were produced during growth on wheat bran and sugar beet pulp, respectively. In addition, Tal. stipitatus produced a new type of esterase (TsFaeC) during growth on sugar beet pulp with a broader spectrum of activity (Type-C) against the (hydroxy)cinnamate esters than those previously described. All three enzymes were purified and N-terminal amino acid sequences and internal peptide sequences determined. The TsFaeC sequences were used to amplify a gene fragment from Tal. stipitatus genomic DNA. The flanking sequences were identified with the aid of RACE-RTPCR, and a full-length clone constructed. The faeC gene is present as a single copy and contains a single intron. The complete cDNA fragment contains an ORF of 1590bp, faeC, which is predicted to encode a 530 amino acid pre-protein, including a 25-residue signal peptide, and to produce a mature protein of M(R) 55 340Da. There was no evidence for a carbohydrate-binding domain in TsFaeC.
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66
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Hatzakis NS, Smonou I. Enantioselectivity and diastereoselectivity in the transesterification of secondary alcohols mediated by feruloyl esterase from Humicola insolens. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.02.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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67
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Vincent F, Yates D, Garman E, Davies GJ, Brannigan JA. The three-dimensional structure of the N-acetylglucosamine-6-phosphate deacetylase, NagA, from Bacillus subtilis: a member of the urease superfamily. J Biol Chem 2003; 279:2809-16. [PMID: 14557261 DOI: 10.1074/jbc.m310165200] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The enzyme N-acetylglucosamine-6-phosphate deacetylase, NagA, catalyzes the hydrolysis of the N-acetyl group of GlcNAc-6-P to yield glucosamine 6-phosphate and acetate, the first committed step in the biosynthetic pathway to amino-sugar-nucleotides. It is classified into carbohydrate esterase family CE-9 (see afmb.cnrs-mrs.fr/CAZY/). Here we report the cloning, expression, and three-dimensional structure (Protein Data Bank code 1un7) determination by x-ray crystallography of the Bacillus subtilis NagA at a resolution of 2.0 A. The structure presents two domains, a (beta/alpha)(8) barrel enclosing the active center and a small beta barrel domain. The structure is dimeric, and the substrate phosphate coordination at the active center is provided by an Arg/His pair contributed from the second molecule of the dimer. Both the overall structure and the active center bear a striking similarity to the urease superfamily with two metals involved in substrate binding and catalysis. PIXE (Proton-Induced x-ray Emission) data show that iron is the predominant metal in the purified protein. We propose a catalytic mechanism involving proton donation to the leaving group by aspartate, nucleophilic attack by an Fe-bridged hydroxide, and stabilization of the carbonyl oxygen by one of the two Fe atoms of the pair. We believe that this is the first sugar deacetylase to utilize this fold and catalytic mechanism.
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Affiliation(s)
- Florence Vincent
- Department of Chemistry, The University of York, Heslington, York, YO10 5YW, United Kingdom
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68
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Biely P, Wong KKY, Suckling ID, Spániková S. Transacetylations to carbohydrates catalyzed by acetylxylan esterase in the presence of organic solvent. Biochim Biophys Acta Gen Subj 2003; 1623:62-71. [PMID: 14572903 DOI: 10.1016/s0304-4165(03)00154-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Various conditions were applied to test the ability of acetylxylan esterase (AcXE) from Schizophyllum commune to catalyze acetyl group transfer to methyl beta-D-xylopyranoside (Me-beta-Xylp) and other carbohydrates. The best performance of the enzyme was observed in an n-hexane-vinyl acetate-sodium dioctylsulfosuccinate (DOSS)-water microemulsion at a molar water-detergent ratio (w(0)) of about 4-5. Although the enzyme was found to have a half-life of about 1 h in the system, more than 60% conversion of Me-beta-Xylp to acetylated derivatives was achieved. Under identical reaction conditions, the enzyme acetylated other carbohydrates such as methyl beta-D-cellobioside (Me-beta-Cel), cellotetraose, methyl beta-D-glucopyranoside (Me-beta-Glcp), 2-deoxy-D-glucose, D-mannose, beta-1,4-mannobiose, -mannopentaose, -mannohexaose, beta-1,4-xylobiose and -xylopentaose. This work is the first example of reverse reactions by an acetylxylan esterase and a carbohydrate esterase belonging to family 1.
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Affiliation(s)
- Peter Biely
- PAPRO Forest Research, Sala Street, Private Bag 3020, Rotorua, New Zealand.
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69
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Rumbold K, Biely P, Mastihubová M, Gudelj M, Gübitz G, Robra KH, Prior BA. Purification and properties of a feruloyl esterase involved in lignocellulose degradation by Aureobasidium pullulans. Appl Environ Microbiol 2003; 69:5622-6. [PMID: 12957952 PMCID: PMC194929 DOI: 10.1128/aem.69.9.5622-5626.2003] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The lignocellulolytic fungus Aureobasidium pullulans NRRL Y 2311-1 produces feruloyl esterase activity when grown on birchwood xylan. Feruloyl esterase was purified from culture supernatant by ultrafiltration and anion-exchange, hydrophobic interaction, and gel filtration chromatography. The pure enzyme is a monomer with an estimated molecular mass of 210 kDa in both native and denatured forms and has an apparent degree of glycosylation of 48%. The enzyme has a pI of 6.5, and maximum activity is observed at pH 6.7 and 60 degrees C. Specific activities for methyl ferulate, methyl p-coumarate, methyl sinapate, and methyl caffeate are 21.6, 35.3, 12.9, and 30.4 micro mol/min/mg, respectively. The pure feruloyl esterase transforms both 2-O and 5-O arabinofuranosidase-linked ferulate equally well and also shows high activity on the substrates 4-O-trans-feruloyl-xylopyranoside, O-[5-O-[(E)-feruloyl]-alpha-L-arabinofuranosyl]-(1,3)-O-beta-D-xylopyranosyl-(1,4)-D-xylopyranose, and p-nitrophenyl-acetate but reveals only low activity on p-nitrophenyl-butyrate. The catalytic efficiency (k(cat)/K(m)) of the enzyme was highest on methyl p-coumarate of all the substrates tested. Sequencing revealed the following eight N-terminal amino acids: AVYTLDGD.
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Affiliation(s)
- Karl Rumbold
- Department of Microbiology, University of Stellenbosch, 7602 Matieland, South Africa
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70
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Vincent F, Charnock SJ, Verschueren KHG, Turkenburg JP, Scott DJ, Offen WA, Roberts S, Pell G, Gilbert HJ, Davies GJ, Brannigan JA. Multifunctional xylooligosaccharide/cephalosporin C deacetylase revealed by the hexameric structure of the Bacillus subtilis enzyme at 1.9A resolution. J Mol Biol 2003; 330:593-606. [PMID: 12842474 DOI: 10.1016/s0022-2836(03)00632-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Esterases and deacetylases active on carbohydrate ligands have been classified into 14 families based upon amino acid sequence similarities. Enzymes from carbohydrate esterase family seven (CE-7) are unusual in that they display activity towards both acetylated xylooligosaccharides and the antibiotic, cephalosporin C. The 1.9A structure of the multifunctional CE-7 esterase (hereinafter CAH) from Bacillus subtilis 168 reveals a classical alpha/beta hydrolase fold encased within a 32 hexamer. This is the first example of a hexameric alpha/beta hydrolase and is further evidence of the versatility of this particular fold, which is used in a wide variety of biological contexts. A narrow entrance tunnel leads to the centre of the molecule, where the six active-centre catalytic triads point towards the tunnel interior and thus are sequestered away from cytoplasmic contents. By analogy to self-compartmentalising proteases, the tunnel entrance may function to hinder access of large substrates to the poly-specific active centre. This would explain the observation that the enzyme is active on a variety of small, acetylated molecules. The structure of an active site mutant in complex with the reaction product, acetate, reveals details of the putative oxyanion binding site, and suggests that substrates bind predominantly through non-specific contacts with protein hydrophobic residues. Protein residues involved in catalysis are tethered by interactions with protein excursions from the canonical alpha/beta hydrolase fold. These excursions also mediate quaternary structure maintenance, so it would appear that catalytic competence is only achieved on protein multimerisation. We suggest that the acetyl xylan esterase (EC 3.1.1.72) and cephalosporin C deacetylase (EC 3.1.1.41) enzymes of the CE-7 family represent a single class of proteins with a multifunctional deacetylase activity against a range of small substrates.
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Affiliation(s)
- Florence Vincent
- Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5YW, UK
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71
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Chen Y, Rice PA. The role of the conserved Trp330 in Flp-mediated recombination. Functional and structural analysis. J Biol Chem 2003; 278:24800-7. [PMID: 12716882 DOI: 10.1074/jbc.m300853200] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The active site of Flp contains, in addition to a transdonated nucleophilic tyrosine, five other residues that are highly conserved within the lambda-integrase family of site-specific recombinases and the type IB topoisomerases. We have used site-directed mutagenesis and x-ray crystallography to investigate the roles of two such residues, Lys223 and Trp330. Our findings agree with studies on related enzymes showing the importance of Lys223 in catalysis but demonstrate that in Flp-mediated recombination the primary role of Trp330 is architectural rather than catalytic. Eliminating the hydrogen bonding potential of Trp330 by phenylalanine substitution results in surprisingly small changes in reaction rates, compared with dramatic decreases in the activities of W330A, W330H, and W330Q. The structure of a W330F mutant-DNA complex reveals an active site nearly identical to that of the wild type. The phenylalanine side chain preserves most of the van der Waals interactions Trp330 forms with the Tyr343-containing trans helix, which may be particularly important for the docking of this helix. Our studies of Trp330 provide the first detailed examination of this conserved residue in the lambda-integrase family, suggesting that the relative importance of active site residues may differ among Flp and related enzymes.
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Affiliation(s)
- Yu Chen
- Department of Biochemistry and Molecular Biology, the University of Chicago, Illinois 60637, USA
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72
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Abstract
Hemicellulases are a diverse group of enzymes that hydrolyze hemicelluloses--one of the most abundant groups of polysaccharide in nature. These enzymes have many biotechnological applications and their structure/function relationships are a subject of intense research. During the past year, new high-resolution structures of catalytic and non-catalytic domains of hemicellulases have been elucidated, and, together with biochemical studies, they reveal the principles of catalysis and specificity for these enzymes.
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Affiliation(s)
- Dalia Shallom
- Department of Food Engineering and Biotechnology and Institute of Catalysis, Science and Technology, Technion, Haifa 32000, Israel
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73
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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; 29:176-84. [PMID: 12767807 DOI: 10.1016/s1046-5928(03)00050-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Feruloyl esterases constitute an interesting group of enzymes that have the potential for use over a broad range of applications in the agri-food industries. We report the over-expression and characterization of a novel feruloyl esterase exhibiting broad substrate specificity from Talaromyces stipitatus (FAEC) in Pichia pastoris. Using various gene constructions, we have investigated the use of alternative signal peptides to produce an authentic feruloyl esterase featuring the N-terminal sequence determined for the native enzyme. We demonstrate that additional amino acids at the N-terminus of the FAEC sequence do not influence the catalytic capacity of the enzyme, and that the nature of the signal sequence has a limited effect on the yield of the secreted enzyme, with the T. stipitatus FAEC signal sequence producing 297 mgL(-1), the Neurospora crassa Fae-1 260 mgL(-1), and the Saccharomyces cerevisiae alpha-factor secretion signal 214 mgL(-1). Mature FAEC contains two internal peptide sequences that correspond with the consensus motif G-X-S-X-G that contains the catalytic serine nucleophile, which is conserved in the esterase enzyme superfamily. The serine residues at the center of these peptide motifs have been independently mutated and the corresponding enzymes have been over-expressed in P. pastoris to identify the candidate nucleophilic residue responsible for catalyzing the enzymatic reaction. Purified recombinant FAEC containing S465A retained the esterase activity and appeared unaffected by the amino acid modification. In contrast, FAEC activity containing S166A was below the HPLC detection limit, suggesting that serine 166 constitutes the nucleophile.
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Affiliation(s)
- Valerie F Crepin
- University of Nottingham, School of Biosciences, Division of Food Sciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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74
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Crepin VF, Faulds CB, Connerton IF. A non-modular type B feruloyl esterase from Neurospora crassa exhibits concentration-dependent substrate inhibition. Biochem J 2003; 370:417-27. [PMID: 12435269 PMCID: PMC1223187 DOI: 10.1042/bj20020917] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2002] [Revised: 11/06/2002] [Accepted: 11/18/2002] [Indexed: 11/17/2022]
Abstract
Feruloyl esterases, a subclass of the carboxylic acid esterases (EC 3.1.1.1), are able to hydrolyse the ester bond between the hydroxycinnamic acids and sugars present in the plant cell wall. The enzymes have been classified as type A or type B, based on their substrate specificity for aromatic moieties. We show that Neurospora crassa has the ability to produce multiple ferulic acid esterase activities depending upon the length of fermentation with either sugar beet pulp or wheat bran substrates. A gene identified on the basis of its expression on sugar beet pulp has been cloned and overexpressed in Pichia pastoris. The gene encodes a single-domain ferulic acid esterase, which represents the first report of a non-modular type B enzyme (fae-1 gene; GenBank accession no. AJ293029). The purified recombinant protein has been shown to exhibit concentration-dependent substrate inhibition (K(m) 0.048 mM, K (i) 2.5 mM and V(max) 8.2 units/mg against methyl 3,4-dihydroxycinnamate). The kinetic behaviour of the non-modular enzyme is discussed in terms of the diversity in the roles of the feruloyl esterases in the mobilization of plant cell wall materials and their respective modes of action.
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Affiliation(s)
- Valerie F Crepin
- University of Nottingham, School of Biosciences, Division of Food Sciences, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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75
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Hatzakis NS, Daphnomili D, Smonou I. Ferulic acid esterase from Humicola Insolens catalyzes enantioselective transesterification of secondary alcohols. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s1381-1177(02)00228-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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76
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Nurizzo D, Nagy T, Gilbert HJ, Davies GJ. The structural basis for catalysis and specificity of the Pseudomonas cellulosa alpha-glucuronidase, GlcA67A. Structure 2002; 10:547-56. [PMID: 11937059 DOI: 10.1016/s0969-2126(02)00742-6] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Alpha-glucuronidases, components of an ensemble of enzymes central to the recycling of photosynthetic biomass, remove the alpha-1,2 linked 4-O-methyl glucuronic acid from xylans. The structure of the alpha-glucuronidase, GlcA67A, from Pseudomonas cellulosa reveals three domains, the central of which is a (beta/alpha)(8) barrel housing the catalytic apparatus. Complexes of the enzyme with the individual reaction products, either xylobiose or glucuronic acid, and the ternary complex of both glucuronic acid and xylotriose reveal a "blind" pocket which selects for short decorated xylooligosaccharides substituted with the uronic acid at their nonreducing end, consistent with kinetic data. The catalytic center reveals a constellation of carboxylates; Glu292 is poised to provide protonic assistance to leaving group departure with Glu393 and Asp365 both appropriately positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water.
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Affiliation(s)
- Didier Nurizzo
- Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, United Kingdom
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