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Lipsh-Sokolik R, Khersonsky O, Schröder SP, de Boer C, Hoch SY, Davies GJ, Overkleeft HS, Fleishman SJ. Combinatorial assembly and design of enzymes. Science 2023; 379:195-201. [PMID: 36634164 DOI: 10.1126/science.ade9434] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The design of structurally diverse enzymes is constrained by long-range interactions that are necessary for accurate folding. We introduce an atomistic and machine learning strategy for the combinatorial assembly and design of enzymes (CADENZ) to design fragments that combine with one another to generate diverse, low-energy structures with stable catalytic constellations. We applied CADENZ to endoxylanases and used activity-based protein profiling to recover thousands of structurally diverse enzymes. Functional designs exhibit high active-site preorganization and more stable and compact packing outside the active site. Implementing these lessons into CADENZ led to a 10-fold improved hit rate and more than 10,000 recovered enzymes. This design-test-learn loop can be applied, in principle, to any modular protein family, yielding huge diversity and general lessons on protein design principles.
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Affiliation(s)
- R Lipsh-Sokolik
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - O Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - S P Schröder
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - C de Boer
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S-Y Hoch
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - G J Davies
- York Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York YO10 5DD, UK
| | - H S Overkleeft
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, Netherlands
| | - S J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel
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2
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Vacilotto MM, Pellegrini VOA, Sepulchro AGV, Capetti CCDM, Curvelo AAS, Marcondes WF, Arantes V, Polikarpov I. Paludibacter propionicigenes GH10 xylanase as a tool for enzymatic xylooligosaccharides production from heteroxylans. Carbohydr Polym 2022; 275:118684. [PMID: 34742414 DOI: 10.1016/j.carbpol.2021.118684] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/30/2021] [Accepted: 09/16/2021] [Indexed: 12/17/2022]
Abstract
Bioconversion of lignocellulosic biomass into value-added products relies on polysaccharides depolymerization by carbohydrate active enzymes. This work reports biochemical characterization of Paludibacter propionicigenes xylanase from GH10 (PpXyn10A) and its application for enzymatic xylooligosaccharides (XOS) production from commercial heteroxylans and liquor of hydrothermally pretreated corn cobs (PCC). PpXyn10A is tolerant to ethanol and NaCl, and releases xylobiose (X2) and xylotriose (X3) as the main hydrolytic products. The conversion rate of complex substrates into short XOS was approximately 30% for glucuronoxylan and 8.8% for rye arabinoxylan, after only 4 h; while for PCC, PpXyn10A greatly increased unbranched XOS yields. B. adolescentis fermentation with XOS from beechwood glucuronoxylan produced mainly acetic and lactic acids. Structural analysis shows that while the glycone region of PpXyn10A active site is well preserved, the aglycone region has aromatic interactions in the +2 subsite that may explain why PpXyn10A does not release xylose.
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Affiliation(s)
- Milena Moreira Vacilotto
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Vanessa O Arnoldi Pellegrini
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Ana Gabriela Veiga Sepulchro
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Caio C de Mello Capetti
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Antonio Aprigio S Curvelo
- Instituto de Química de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil
| | - Wilian Fioreli Marcondes
- Biocatalysis and Bioproducts Laboratory, Department of Biotechnology, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP, Brazil
| | - Valdeir Arantes
- Biocatalysis and Bioproducts Laboratory, Department of Biotechnology, Escola de Engenharia de Lorena, Universidade de São Paulo, Lorena, SP, Brazil
| | - Igor Polikarpov
- Instituto de Física de São Carlos, Universidade de São Paulo, Avenida Trabalhador São-carlense 400, 13566-590 São Carlos, SP, Brazil.
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3
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Sepulchro AGV, Pellegrini VO, Briganti L, de Araujo EA, de Araujo SS, Polikarpov I. Transformation of xylan into value-added biocommodities using Thermobacillus composti GH10 xylanase. Carbohydr Polym 2020; 247:116714. [DOI: 10.1016/j.carbpol.2020.116714] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/13/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022]
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4
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Li K, Qi H, Liu Q, Li T, Chen W, Li S, Piao HL, Yin H. Preparation and antitumor activity of selenium-modified glucomannan oligosaccharides. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103731] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
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5
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Oven drying and hot water cooking processes decrease HCN contents of cassava leaves. Food Res Int 2019; 119:517-523. [DOI: 10.1016/j.foodres.2019.01.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/10/2019] [Accepted: 01/13/2019] [Indexed: 11/22/2022]
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6
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Niderhaus C, Garrido M, Insani M, Campos E, Wirth S. Heterologous production and characterization of a thermostable GH10 family endo-xylanase from Pycnoporus sanguineus BAFC 2126. Process Biochem 2018. [DOI: 10.1016/j.procbio.2018.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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7
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Saxena H, Hsu B, de Asis M, Zierke M, Sim L, Withers SG, Wakarchuk W. Characterization of a thermostable endoglucanase from Cellulomonas fimi ATCC484. Biochem Cell Biol 2017; 96:68-76. [PMID: 28982013 DOI: 10.1139/bcb-2017-0150] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bacteria in the genus Cellulomonas are well known as secretors of a variety of mesophilic carbohydrate degrading enzymes (e.g., cellulases and hemicellulases), active against plant cell wall polysaccharides. Recent proteomic analysis of the mesophilic bacterium Cellulomonas fimi ATCC484 revealed uncharacterized enzymes for the hydrolysis of plant cell wall biomass. Celf_1230 (CfCel6C), a secreted protein of Cellulomonas fimi ATCC484, is a novel member of the GH6 family of cellulases that could be successfully expressed in Escherichia coli. This enzyme displayed very little enzymatic/hydrolytic activity at 30 °C, but showed an optimal activity around 65 °C, and exhibited a thermal denaturation temperature of 74 °C. In addition, it also strongly bound to filter paper despite having no recognizable carbohydrate binding module. Our experiments show that CfCel6C is a thermostable endoglucanase with activity on a variety of β-glucans produced by an organism that struggles to grow above 30 °C.
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Affiliation(s)
- Hirak Saxena
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Bryan Hsu
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Marc de Asis
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
| | - Mirko Zierke
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lyann Sim
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Stephen G Withers
- b Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Warren Wakarchuk
- a Department of Chemistry and Biology, Ryerson University, Toronto, ON M5B 2K3, Canada
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8
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Álvarez-Cervantes J, Díaz-Godínez G, Mercado-Flores Y, Gupta VK, Anducho-Reyes MA. Phylogenetic analysis of β-xylanase SRXL1 of Sporisorium reilianum and its relationship with families (GH10 and GH11) of Ascomycetes and Basidiomycetes. Sci Rep 2016; 6:24010. [PMID: 27040368 PMCID: PMC4819176 DOI: 10.1038/srep24010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
In this paper, the amino acid sequence of the β-xylanase SRXL1 of Sporisorium reilianum, which is a pathogenic fungus of maize was used as a model protein to find its phylogenetic relationship with other xylanases of Ascomycetes and Basidiomycetes and the information obtained allowed to establish a hypothesis of monophyly and of biological role. 84 amino acid sequences of β-xylanase obtained from the GenBank database was used. Groupings analysis of higher-level in the Pfam database allowed to determine that the proteins under study were classified into the GH10 and GH11 families, based on the regions of highly conserved amino acids, 233-318 and 180-193 respectively, where glutamate residues are responsible for the catalysis.
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Affiliation(s)
| | - Gerardo Díaz-Godínez
- Laboratory of Biotechnology, Research Center for Biological Sciences, Universidad Autónoma de Tlaxcala, Tlaxcala, México
| | | | - Vijai Kumar Gupta
- Molecular Glycobiotechnology Group, Discipline of Biochemistry, National University of Ireland Galway, Galway, Ireland
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9
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Secretion of recombinant thermo-alkali-stable endoxylanase of polyextremophilic Bacillus halodurans TSEV1 and its utility in generating xylooligosaccharides from renewable agro-residues. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.08.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Kallemeijn WW, Witte MD, Voorn-Brouwer TM, Walvoort MTC, Li KY, Codée JDC, van der Marel GA, Boot RG, Overkleeft HS, Aerts JMFG. A sensitive gel-based method combining distinct cyclophellitol-based probes for the identification of acid/base residues in human retaining β-glucosidases. J Biol Chem 2014; 289:35351-62. [PMID: 25344605 DOI: 10.1074/jbc.m114.593376] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Retaining β-exoglucosidases operate by a mechanism in which the key amino acids driving the glycosidic bond hydrolysis act as catalytic acid/base and nucleophile. Recently we designed two distinct classes of fluorescent cyclophellitol-type activity-based probes (ABPs) that exploit this mechanism to covalently modify the nucleophile of retaining β-glucosidases. Whereas β-epoxide ABPs require a protonated acid/base for irreversible inhibition of retaining β-glucosidases, β-aziridine ABPs do not. Here we describe a novel sensitive method to identify both catalytic residues of retaining β-glucosidases by the combined use of cyclophellitol β-epoxide- and β-aziridine ABPs. In this approach putative catalytic residues are first substituted to noncarboxylic amino acids such as glycine or glutamine through site-directed mutagenesis. Next, the acid/base and nucleophile can be identified via classical sodium azide-mediated rescue of mutants thereof. Selective labeling with fluorescent β-aziridine but not β-epoxide ABPs identifies the acid/base residue in mutagenized enzyme, as only the β-aziridine ABP can bind in its absence. The Absence of the nucleophile abolishes any ABP labeling. We validated the method by using the retaining β-glucosidase GBA (CAZy glycosylhydrolase family GH30) and then applied it to non-homologous (putative) retaining β-glucosidases categorized in GH1 and GH116: GBA2, GBA3, and LPH. The described method is highly sensitive, requiring only femtomoles (nanograms) of ABP-labeled enzymes.
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Affiliation(s)
- Wouter W Kallemeijn
- From the Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands and
| | - Martin D Witte
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Tineke M Voorn-Brouwer
- From the Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands and
| | - Marthe T C Walvoort
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Kah-Yee Li
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Jeroen D C Codée
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Gijsbert A van der Marel
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Rolf G Boot
- From the Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands and
| | - Herman S Overkleeft
- Bioorganic Synthesis, Leiden Institute of Chemistry, P. O. box 9502, 2300 RA Leiden, The Netherlands
| | - Johannes M F G Aerts
- From the Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands and
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11
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A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation. Biosci Biotechnol Biochem 2014; 76:215-31. [DOI: 10.1271/bbb.110713] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Han Q, Liu N, Robinson H, Cao L, Qian C, Wang Q, Xie L, Ding H, Wang Q, Huang Y, Li J, Zhou Z. Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain. Biotechnol Bioeng 2013; 110:3093-103. [PMID: 23794438 DOI: 10.1002/bit.24982] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/15/2013] [Accepted: 06/10/2013] [Indexed: 11/11/2022]
Abstract
Bacterial Ig-like (Big) domains are commonly distributed in glycoside hydrolases (GH), but their structure and function remains undefined. Xylanase is a GH, and catalyzes the hydrolysis of the internal β-xylosidic linkages of xylan. In this study, we report the molecular cloning, biochemical and biophysical characterization, and crystal structure of a termite gut bacterial xylanase, Xyl-ORF19, which was derived from gut bacteria of a wood-feeding termite (Globitermes brachycerastes). The protein architecture of Xyl-ORF19 reveals that it has two domains, a C-terminal GH10 catalytic domain and an N-terminal Big_2 non-catalytic domain. The catalytic domain folds in an (α/β)8 barrel as most GH10 xylanases do, but it has two extra β-strands. The non-catalytic domain is structurally similar to an immunoglobulin-like domain of intimins. The recombinant enzyme without the non-catalytic domain has fairly low catalytic activity, and is different from the full-length enzyme in kinetic parameters, pH and temperature profiles, which suggests the non-catalytic domain could affect the enzyme biochemical and biophysical properties as well as the role for enzyme localization. This study provides a molecular basis for future efforts in xylanase bioengineering.
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Affiliation(s)
- Qian Han
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, 24061
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13
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Cloning, purification and characterization of an alkali-stable endoxylanase from thermophilic Geobacillus sp. 71. World J Microbiol Biotechnol 2012; 28:1981-8. [DOI: 10.1007/s11274-011-1000-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 12/31/2011] [Indexed: 11/25/2022]
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14
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A novel thermostable and glucose-tolerant β-glucosidase from Fervidobacterium islandicum. Appl Microbiol Biotechnol 2011; 93:1947-56. [DOI: 10.1007/s00253-011-3406-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/19/2011] [Accepted: 05/19/2011] [Indexed: 10/14/2022]
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15
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Tseng CW, Ko TP, Guo RT, Huang JW, Wang HC, Huang CH, Cheng YS, Wang AHJ, Liu JR. Substrate binding of a GH5 endoglucanase from the ruminal fungus Piromyces rhizinflata. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1189-94. [PMID: 22102024 PMCID: PMC3212359 DOI: 10.1107/s1744309111032428] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 08/10/2011] [Indexed: 11/11/2022]
Abstract
The endoglucanase EglA from Piromyces rhizinflata found in cattle stomach belongs to the GH5 family of glycoside hydrolases. The crystal structure of the catalytic domain of EglA shows the (β/α)(8)-barrel fold typical of GH5 enzymes. Adjacent to the active site of EglA, a loop containing a disulfide bond not found in other similar structures may participate in substrate binding. Because the active site was blocked by the N-terminal His tag of a neighbouring protein molecule in the crystal, enzyme-substrate complexes could not be obtained by soaking but were prepared by cocrystallization. The E154A mutant structure with a cellotriose bound to the -3, -2 and -1 subsites shows an extensive hydrogen-bonding network between the enzyme and the substrate, along with a stacking interaction between Trp44 and the -3 sugar. A possible dimer was observed in the crystal structure, but retention of activity in the E242A mutant suggested that the enzyme probably does not function as a dimer in solution. On the other hand, the first 100 amino acids encoded by the original cDNA fragment are very similar to those in the last third of the (β/α)(8)-barrel fold, indicating that EglA comprises at least two catalytic domains acting in tandem.
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Affiliation(s)
- Chih-Wen Tseng
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Rey-Ting Guo
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Jian-Wen Huang
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Hao-Ching Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Hsiang Huang
- Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, People’s Republic of China
| | - Ya-Shan Cheng
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
| | - Andrew H.-J. Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Je-Ruei Liu
- Institute of Biotechnology, National Taiwan University, Taipei 10617, Taiwan
- Department of Animal Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan
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16
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Goddard-Borger ED, Fiege B, Kwan EM, Withers SG. Glycosynthase-Mediated Assembly of Xylanase Substrates and Inhibitors. Chembiochem 2011; 12:1703-11. [DOI: 10.1002/cbic.201100229] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Indexed: 11/09/2022]
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17
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Bahari L, Gilad Y, Borovok I, Kahel-Raifer H, Dassa B, Nataf Y, Shoham Y, Lamed R, Bayer EA. Glycoside hydrolases as components of putative carbohydrate biosensor proteins in Clostridium thermocellum. J Ind Microbiol Biotechnol 2010; 38:825-32. [DOI: 10.1007/s10295-010-0848-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2010] [Accepted: 08/16/2010] [Indexed: 11/28/2022]
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18
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Li R, Kibblewhite R, Orts WJ, Lee CC. Molecular cloning and characterization of multidomain xylanase from manure library. World J Microbiol Biotechnol 2009. [DOI: 10.1007/s11274-009-0111-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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20
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Febbraio F, D'Andrea SE, Mandrich L, Merone L, Rossi M, Nucci R, Manco G. Irreversible inhibition of the thermophilic esterase EST2 from Alicyclobacillus acidocaldarius. Extremophiles 2008; 12:719-28. [PMID: 18622571 DOI: 10.1007/s00792-008-0179-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2008] [Accepted: 06/18/2008] [Indexed: 12/18/2022]
Abstract
Kinetic studies of irreversible inhibition in recent years have received growing attention owing to their relevance to problems of basic scientific interest as well as to their practical importance. Our studies have been devoted to the characterization of the effects that well-known acetylcholinesterase irreversible inhibitors exert on a carboxylesterase (EST2) from the thermophilic eubacterium Alicyclobacillus acidocaldarius. In particular, sulfonyl inhibitors and the organophosphorous insecticide diethyl-p-nitrophenyl phosphate (paraoxon) have been studied. The incubation of EST2 with sulfonyl inhibitors resulted in a time-dependent inactivation according to a pseudo-first-order kinetics. On the other hand, the EST2 inactivation process elicited by paraoxon, being the inhibition reaction completed immediately after the inhibitor addition, cannot be described as a pseudo-first-order kinetics but is better considered as a high affinity inhibition. The values of apparent rate constants for paraoxon inactivation were determined by monitoring the enzyme/substrate reaction in the presence of the inhibitor, and were compared with those of the sulfonyl inhibitors. The protective effect afforded by a competitive inhibitor on the EST2 irreversible inhibition, and the reactivation of a complex enzyme/irreversible-inhibitor by hydroxylamine and 2-PAM, were also investigated. The data have been discussed in the light of the recently described dual substrate binding mode of EST2, considering that the irreversible inhibitors employed were able to discriminate between the two different binding sites.
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Affiliation(s)
- Ferdinando Febbraio
- Istituto di Biochimica delle Proteine, CNR, Via P. Castellino 111, 80131 Naples, Italy.
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21
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Sakamoto T, Taniguchi Y, Suzuki S, Ihara H, Kawasaki H. Characterization of Fusarium oxysporum beta-1,6-galactanase, an enzyme that hydrolyzes larch wood arabinogalactan. Appl Environ Microbiol 2007; 73:3109-12. [PMID: 17351093 PMCID: PMC1892885 DOI: 10.1128/aem.02101-06] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A type II arabinogalactan-degrading enzyme (FoGal1) was purified from Fusarium oxysporum 12S, and the corresponding cDNA was isolated. FoGal1 had high similarity to enzymes of glycoside hydrolase family 5. Treatment of larch wood arabinogalactan with the recombinant enzyme indicated that FoGal1 is a beta-1,6-galactanase that preferentially debranches beta-1,6-galactobiose from the substrate.
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Affiliation(s)
- Tatsuji Sakamoto
- Division of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka 599-8531, Japan.
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22
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Poon DKY, Schubert M, Au J, Okon M, Withers SG, McIntosh LP. Unambiguous determination of the ionization state of a glycoside hydrolase active site lysine by 1H-15N heteronuclear correlation spectroscopy. J Am Chem Soc 2007; 128:15388-9. [PMID: 17132001 DOI: 10.1021/ja065766z] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the lysine side chain amines in the 34 kDa catalytic domain from Cellulomonas fimi beta-(1,4)-glycosidase Cex (or CfXyn10A) using 1H-detected 15N heteronuclear correlation NMR spectroscopy. Signals from the 1Hzeta ( approximately 8 ppm) and 15Nzeta ( approximately 35 ppm) of Lys302 in the unmodified enzyme and Lys47 in a trapped cellobiosyl-enzyme intermediate were detected in a 1H-15N HMQC spectrum (pH 6.5 and 30 degrees C). The amine of Lys302 forms a buried ion pair, and that of Lys47 is hydrogen bonded to the cellobioside. Both lysines are positively charged, as unambiguously demonstrated by the splitting of their 15Nzeta signals into quartets (|1JNH| approximately 75 Hz) in a 1H-15N HSQC spectrum recorded without 1H decoupling during 15N evolution. Qualitative insights into the dynamic properties of these lysines are also provided by the deviations of their quartet intensity ratios from that of approximately 3:1:1:3 expected for a highly mobile amine. On the basis of the observed ratios of approximately 1:1:1:1 for the quartet of Lys302 and approximately 0.5:1:1:0.5 for Lys47, the amine of the latter active site residue is most rigidly positioned. Signals from at least 8 and 10 additional positively charged, mobile amines in Cex were observed at 10 degrees C and pH 6.5 and 5.6, respectively. By using conditions of reduced temperature, slightly acidic pH, and low general base concentrations, as well as water flipback pulses to minimize the effects of hydrogen exchange, 1H-15N correlation experiments provide a sensitive route to directly investigate the charge states and dynamic properties of the N-terminal and side chain amines in proteins and protein complexes.
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Affiliation(s)
- David K Y Poon
- Department of Biochemistry and Molecular Biology, The Protein Engineering Network of Centres of Excellence, and The Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
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23
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Identification and molecular modeling of a family 5 endocellulase from Thermus caldophilus GK24, a cellulolytic strain of Thermus thermophilus. Int J Mol Sci 2006. [DOI: 10.3390/i7120571] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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24
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Gloster TM, Madsen R, Davies GJ. Structural basis for cyclophellitol inhibition of a beta-glucosidase. Org Biomol Chem 2006; 5:444-6. [PMID: 17252125 DOI: 10.1039/b616590g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structural basis for beta-glucosidase inhibition by cyclophellitol is demonstrated using X-ray crystallography, enzyme kinetics and mass spectrometry.
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Affiliation(s)
- Tracey M Gloster
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, UK YO10 5YW
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25
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Tanaka H, Muguruma M, Ohta K. Purification and properties of a family-10 xylanase from Aureobasidium pullulans ATCC 20524 and characterization of the encoding gene. Appl Microbiol Biotechnol 2006; 70:202-11. [PMID: 15988573 DOI: 10.1007/s00253-005-0045-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2005] [Revised: 05/02/2005] [Accepted: 05/30/2005] [Indexed: 10/25/2022]
Abstract
An extracellular endo-1,4-beta-xylanase was purified from the culture supernatant of the ascomycete Aureobasidium pullulans ATCC 20524 grown on xylan. The purified enzyme was homogeneous as judged by sodium dodecyl sulphate-polyacrylamide gel electrophoresis and isoelectric focusing, which showed an apparent M (r) of 39 kDa and a pI of 8.9, respectively. Xylanase activity was optimal at pH 6.0 and 70 degrees C. The genomic DNA and cDNAs encoding this protein were cloned and sequenced. The xylanase gene (xynII) encoded a 26 amino acid signal peptide and a 335 amino acid mature protein. DNA regions encoding the signal sequence and the mature protein were interrupted by introns of 56 and 73 bp, respectively. The xynII 5'-noncoding region had two consensus binding sites (5'-GCCARG-3') for the transcription factor PacC mediating pH regulation. Quantitative real-time polymerase chain reaction analysis revealed that the transcription levels at pH 6.0 and 8.0 were 8-fold and 22-fold higher than that at pH 2.7, respectively. A cloned xynII cDNA was expressed and secreted in the yeast Pichia pastoris. Sequence alignment and phylogenetic analysis suggested that the XynII belongs to glycosyl hydrolase family 10 and that it is evolutionarily distant from two clusters formed by other family-10 xylanases.
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Affiliation(s)
- Hidenori Tanaka
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, University of Miyazaki, Japan
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26
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Lee CC, Smith M, Kibblewhite-Accinelli RE, Williams TG, Wagschal K, Robertson GH, Wong DWS. Isolation and Characterization of a Cold-Active Xylanase Enzyme from Flavobacterium sp. Curr Microbiol 2006; 52:112-6. [PMID: 16450065 DOI: 10.1007/s00284-005-4583-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 08/29/2005] [Indexed: 10/25/2022]
Abstract
Xylan is the major component of hemicellulose, and xylan should be fully utilized to improve the efficiencies of a biobased economy. There are a variety of industrial reaction conditions in which an active xylanase enzyme would be desired. As a result, xylanase enzymes with different activity profiles are of great interest. We isolated a xylanase gene (xyn10) from a Flavobacterium sp. whose sequence suggests that it is a glycosyl hydrolase family 10 member. The enzyme has a temperature optimum of 30 degrees C, is active at cold temperatures, and is thermolabile. The enzyme has an apparent Km of 1.8 mg/ml and kcat of 100 sec-1 for beechwood xylan, attacks highly branched native xylan substrates, and does not have activity against glucans.
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Affiliation(s)
- Charles C Lee
- United States Department of Agriculture, Agricultural Research Service, Western Regional Research Center, 800 Buchanan St., Albany, CA 94710, USA.
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27
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Nishimoto M, Kitaoka M, Fushinobu S, Hayashi K. The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases. Biosci Biotechnol Biochem 2005; 69:904-10. [PMID: 15914908 DOI: 10.1271/bbb.69.904] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An arginine residue in loop 4 connecting beta strand 4 and alpha-helix 4 is conserved in glycoside hydrolase family 10 (GH10) xylanases. The arginine residues, Arg(204) in xylanase A from Bacillus halodurans C-125 (XynA) and Arg(196) in xylanase B from Clostridium stercorarium F9 (XynB), were replaced by glutamic acid, lysine, or glutamine residues (XynA R204E, K and Q, and XynB R196E, K and Q). The pH-k(cat)/K(m) and the pH-k(cat) relationships of these mutant enzymes were measured. The pK(e2) and pK(es2) values calculated from these curves were 8.59 and 8.29 (R204E), 8.59 and 8.10 (R204K), 8.61 and 8.19 (R204Q), 7.42 and 7.19 (R196E), 7.49 and 7.18 (R196K), and 7.86 and 7.38 (R196Q) respectively. Only the pK(es2) value of arginine derivatives was less than those of the wild types (8.49 and 9.39 [XynA] and 7.62 and 7.82 [XynB]). These results suggest that the conserved arginine residue in GH10 xylanases increases the pK(a) value of the proton donor Glu during substrate binding. The arginine residue is considered to clamp the proton donor and subsite +1 to prevent structural change during substrate binding.
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28
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Hekmat O, Kim YW, Williams SJ, He S, Withers SG. Active-site peptide "fingerprinting" of glycosidases in complex mixtures by mass spectrometry. Discovery of a novel retaining beta-1,4-glycanase in Cellulomonas fimi. J Biol Chem 2005; 280:35126-35. [PMID: 16085650 DOI: 10.1074/jbc.m508434200] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
New proteomics methods are required for targeting and identification of subsets of a proteome in an activity-based fashion. Here, we report the first gel-free, mass spectrometry-based strategy for mechanism-based profiling of retaining beta-endoglycosidases in complex proteomes. Using a biotinylated, cleavable 2-deoxy-2-fluoroxylobioside inactivator, we have isolated and identified the active-site peptides of target retaining beta-1,4-glycanases in systems of increasing complexity: pure enzymes, artificial proteomes, and the secreted proteome of the aerobic mesophilic soil bacterium Cellulomonas fimi. The active-site peptide of a new C. fimi beta-1,4-glycanase was identified in this manner, and the peptide sequence, which includes the catalytic nucleophile, is highly conserved among glycosidase family 10 members. The glycanase gene (GenBank accession number DQ146941) was cloned using inverse PCR techniques, and the protein was found to comprise a catalytic domain that shares approximately 70% sequence identity with those of xylanases from Streptomyces sp. and a family 2b carbohydrate-binding module. The new glycanase hydrolyzes natural and artificial xylo-configured substrates more efficiently than their cello-configured counterparts. It has a pH dependence very similar to that of known C. fimi retaining glycanases.
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Affiliation(s)
- Omid Hekmat
- Protein Engineering Network of Centres of Excellence of Canada, Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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29
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Han SO, Yukawa H, Inui M, Doi RH. Isolation and expression of the xynB gene and its product, XynB, a consistent component of the Clostridium cellulovorans cellulosome. J Bacteriol 2005; 186:8347-55. [PMID: 15576784 PMCID: PMC532426 DOI: 10.1128/jb.186.24.8347-8355.2004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nucleotide sequence of the Clostridium cellulovorans xynB gene, which encodes the XynB xylanase, consists of 1,821 bp and encodes a protein of 607 amino acids with a molecular weight of 65,976. XynB contains a typical N-terminal signal peptide of 29 amino acid residues, followed by a 147-amino-acid sequence that is homologous to the family 4-9 (subfamily 9 in family 4) carbohydrate-binding domain. Downstream of this domain is a family 10 catalytic domain of glycosyl hydrolase. The C terminus separated from the catalytic domain by a short linker sequence contains a dockerin domain responsible for cellulosome assembly. The XynB sequence from mass spectrometry and N-terminal amino acid sequence analyses agreed with that deduced from the nucleotide sequence. XynB was highly active toward xylan, but not active toward carboxymethyl cellulose. The enzyme was optimally active at 40 degrees C and pH 5.0. Northern hybridizations revealed that xynB is transcribed as a monocistronic 1.9-kb mRNA. RNA ligase-mediated rapid amplification of 5' cDNA ends by PCR (RLM-5'RACE PCR) analysis of C. cellulovorans RNA identified a single transcriptional start site of xynB located 47 bp upstream from the first nucleotide of the translation initiation codon. Alignment of the xynB promoter region provided evidence for highly conserved sequences that exhibited strong similarity to the sigmaA consensus promoter sequences of gram-positive bacteria. Expression of xynB mRNA increased from early to middle exponential phase and decreased during the early stationary phase when the cells were grown on cellobiose. No alternative promoter was observed by RLM-5'RACE PCR and reverse transcriptase PCR analyses during expression. The analysis of the products from xylan hydrolysis by thin-layer chromatography indicated its endoxylanase activity. The results suggest that XynB is a consistent and major cellulosomal enzyme during growth on cellulose or xylan.
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Affiliation(s)
- Sung Ok Han
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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30
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Jiang D, Ghabrial SA. Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus. J Gen Virol 2004; 85:2111-2121. [PMID: 15218197 DOI: 10.1099/vir.0.79842-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Molecular cloning and complete nucleotide sequencing of Penicillium chrysogenum virus (PcV) dsRNAs indicated that PcV virions contained four dsRNA segments with sizes of 3562, 3200, 2976 and 2902 bp. Each dsRNA segment had unique sequences and contained a single large open reading frame (ORF). In vitro translation of transcripts derived from full-length cDNA clones of PcV dsRNAs yielded single products of sizes similar to those predicted from the deduced amino acid sequences of the individual ORFs. Sequence similarity searches revealed that dsRNA1 encodes a putative RNA-dependent RNA polymerase. In this study, it was determined that dsRNA2 encodes the major capsid protein and that p4, encoded by dsRNA4, is virion-associated as a minor component. All four dsRNAs of PcV, like the genomic segments of viruses with multipartite genomes, were found to have extended regions of highly conserved terminal sequences at both ends. In addition to the strictly conserved 5'-terminal 10 nt, a second region consisting of reiteration of the sequence CAA was found immediately upstream of the AUG initiator codon. These (CAA)(n) repeats are reminiscent of the translational enhancer elements of tobamoviruses. The 3'-terminal 14 nt were also strictly conserved. As PcV and related viruses with four dsRNA segments (genus Chrysovirus) have not been previously characterized at the molecular level, they were provisionally classified in the family Partitiviridae, comprising viruses with bipartite genomes. This study represents the first report on molecular characterization of a chrysovirus and the results suggest the creation of a new family of mycoviruses with multipartite dsRNA genomes to accommodate PcV and related viruses.
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Affiliation(s)
- Daohong Jiang
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA
| | - Said A Ghabrial
- Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, University of Kentucky, Lexington, KY 40546-0312, USA
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31
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Kaneko S, Ichinose H, Fujimoto Z, Kuno A, Yura K, Go M, Mizuno H, Kusakabe I, Kobayashi H. Structure and function of a family 10 beta-xylanase chimera of Streptomyces olivaceoviridis E-86 FXYN and Cellulomonas fimi Cex. J Biol Chem 2004; 279:26619-26. [PMID: 15078885 DOI: 10.1074/jbc.m308899200] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The catalytic domain of xylanases belonging to glycoside hydrolase family 10 (GH10) can be divided into 22 modules (M1 to M22; Sato, Y., Niimura, Y., Yura, K., and Go, M. (1999) Gene (Amst.) 238, 93-101). Inspection of the crystal structure of a GH10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A) revealed that the catalytic domain of GH10 xylanases can be dissected into two parts, an N-terminal larger region and C-terminal smaller region, by the substrate binding cleft, corresponding to the module border between M14 and M15. It has been suggested that the topology of the substrate binding clefts of GH10 xylanases are not conserved (Charnock, S. J., Spurway, T. D., Xie, H., Beylot, M. H., Virden, R., Warren, R. A. J., Hazlewood, G. P., and Gilbert, H. J. (1998) J. Biol. Chem. 273, 32187-32199). To facilitate a greater understanding of the structure-function relationship of the substrate binding cleft of GH10 xylanases, a chimeric xylanase between SoXyn10A and Xyn10A from Cellulomonas fimi (CfXyn10A) was constructed, and the topology of the hybrid substrate binding cleft established. At the three-dimensional level, SoXyn10A and CfXyn10A appear to possess 5 subsites, with the amino acid residues comprising subsites -3 to +1 being well conserved, although the +2 subsites are quite different. Biochemical analyses of the chimeric enzyme along with SoXyn10A and CfXyn10A indicated that differences in the structure of subsite +2 influence bond cleavage frequencies and the catalytic efficiency of xylooligosaccharide hydrolysis. The hybrid enzyme constructed in this study displays fascinating biochemistry, with an interesting combination of properties from the parent enzymes, resulting in a low production of xylose.
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Affiliation(s)
- Satoshi Kaneko
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan.
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Abstract
Cellulomonas is a unique bacterium possessing not only the capacity to degrade various carbohydrates, such as starch, xylan and cellulose, but crystalline cellulose as well. It has developed a complex battery of glucanases to deal with substrates possessing such extensive microheterogeneities. Some of these enzymes are multifunctional, as well as cross inducible, possessing a multi-domain structure; these enzymes are thought to have arisen by the shuffling of these domains. Intergeneric hybrids have been constructed between Cellulomonas and Zymomonas so as to enhance the industrial potential of this organism. This review examines the unique features of this microorganism and evaluates its key role in the conversion of complex wastes to useful products, by virtue of its unusual attributes.
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Affiliation(s)
- P Chaudhary
- Molecular Biology Research Laboratory, Department of Zoology, University of Poona, Pune-411 007, India
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McCarthy JK, Uzelac A, Davis DF, Eveleigh DE. Improved catalytic efficiency and active site modification of 1,4-beta-D-glucan glucohydrolase A from Thermotoga neapolitana by directed evolution. J Biol Chem 2003; 279:11495-502. [PMID: 14660638 DOI: 10.1074/jbc.m305642200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Thermotoga neapolitana 1,4-beta-d-glucan glucohydrolase A preferentially hydrolyzes cello-oligomers, such as cellotetraose, releasing single glucose moieties from the reducing end of the cello-oligosaccharide chain. Using directed evolution techniques of error-prone PCR and mutant library screening, a variant glucan glucohydrolase has been isolated that hydrolyzes the disaccharide, cellobiose, at a 31% greater rate than its wild type (WT) predecessor. The mutant library, expressed in Escherichia coli, was screened at 85 degrees C for increased hydrolysis of cellobiose, a native substrate rather than a chromogenic analog, using a continuous, thermostable coupled enzyme assay. The V(max) for the mutant was 108 +/- 3 units mg(-1), whereas that of the WT was 75 +/- 2 units mg(-1). The K(m) for both proteins was nearly the same. The k(cat) for the new enzyme increased by 31% and its catalytic efficiency (k(cat)/K(m)) for cellobiose also rose by 31% as compared with the parent. The nucleotide sequence of two positive clones and two null clones identified 11 single base shifts. The nucleotide transition in the most active clone caused an isoleucine to threonine amino acid substitution at position 170. Structural models for I170T and WT proteins were derived by sequence homology with Protein Data Bank code 1BGA from Paenibacillus polymyxa. Analysis of the WT and I170T model structures indicated that the substitution in the mutant enzyme repositioned the conserved catalytic residue Asn-163 and reconfigured entry to the active site.
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Affiliation(s)
- James K McCarthy
- Department of Biochemistry and Microbiology, Cook College, Rutgers, The State University of New Jersey, New Brunswick, New Jersey 08901, USA
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34
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Tarling CA, He S, Sulzenbacher G, Bignon C, Bourne Y, Henrissat B, Withers SG. Identification of the catalytic nucleophile of the family 29 alpha-L-fucosidase from Thermotoga maritima through trapping of a covalent glycosyl-enzyme intermediate and mutagenesis. J Biol Chem 2003; 278:47394-9. [PMID: 12975375 DOI: 10.1074/jbc.m306610200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Fucose-containing glycoconjugates are key antigenic determinants in many biological processes. A change in expression levels of the enzymes responsible for tailoring these glycoconjugates has been associated with many pathological conditions and it is therefore surprising that little information is known regarding the mechanism of action of these important catabolic enzymes. Thermotoga maritima, a thermophilic bacterium, produces a wide range of carbohydrate-processing enzymes including a 52-kDa alpha-L-fucosidase that has 38% sequence identity and 56% similarity to human fucosidases. The catalytic nucleophile of this enzyme was identified to be Asp-224 within the peptide sequence 222WNDMGWPEKGKEDL235 using the mechanism-based covalent inactivator 2-deoxy-2-fluoro-alpha-L-fucosyl fluoride. The 10(4)-fold lower activity (kcat/Km) of the site-directed mutant D224A, and the subsequent rescue of activity upon addition of exogenous nucleophiles, conclusively confirms this assignment. This article presents the first direct identification of the catalytic nucleophile of an alpha-L-fucosidase, a key step in the understanding of these important enzymes.
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Affiliation(s)
- Chris A Tarling
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z1, Canada
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35
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Jun HS, Ha JK, Malburg LM, Verrinder GAM, Forsberg CW. Characteristics of a cluster of xylanase genes in Fibrobacter succinogenes S85. Can J Microbiol 2003; 49:171-80. [PMID: 12795403 DOI: 10.1139/w03-024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Xylanase genes xyn10D, xyn10E, and xyn10B, located sequentially on the Fibrobacter succinogenes S85 chromosome, were separately cloned and their properties characterized. Analysis of the sequences documented that xylanases Xyn10D, Xyn10E, and Xyn10B each consist of an N-terminal catalytic domain (glycosyl hydrolase family 10) and a C-terminal carbohydrate-binding module (CBM, family 6) connected by proline-rich linker sequences. The amino acid sequences exhibited similarities of between 53 and 60%. The xyn10D, xyn10E, and truncated xyn10deltaACBM were expressed in Escherichia coli and purified to homogeneity. The purified Xyn10D, Xyn10E, and Xyn10BdeltaCBM exhibited the same temperature optimum (40 degrees C) and pH optimum (6.5) and the highest specific activity against arabinoxylan, oat spelt xylan, and birchwood xylan, respectively. Xyn10D exhibited an affinity for cellulose and xylan with 47 and 33% binding, respectively, while the truncated Xyn10DdeltaCBM did not bind to the substrates. The main hydrolysis products of the three xylanases acting on oat spelt xylan and arabinoxylan were xylose and xylobiose. RT-PCR analysis showed that the three genes were co-transcribed as a single transcript. Western immunoblot analysis revealed that the three xylanases were expressed at a very low level by F. succinogenes grown on either glucose or cellulose as the source of carbohydrate.
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MESH Headings
- Amino Acid Sequence
- Anaerobiosis
- Cloning, Molecular
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/classification
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/enzymology
- Gram-Negative Anaerobic Straight, Curved, and Helical Rods/genetics
- Hydrogen-Ion Concentration
- Models, Genetic
- Molecular Sequence Data
- Multigene Family
- Recombinant Proteins/chemistry
- Sequence Alignment
- Substrate Specificity
- Temperature
- Transcription, Genetic
- Xylan Endo-1,3-beta-Xylosidase
- Xylosidases/genetics
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Affiliation(s)
- Hyun S Jun
- Department of Microbiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Abstract
The mechanism-based inactivation and subsequent identification of the nucleophilic residue using mass spectrometry have been successfully applied and used to identify the active-site nucleophile in numerous beta-glycosidases, as illustrated using C. fimi exoglycanase. Evidence for a covalent glycosyl-enzyme intermediate has come from X-ray crystallographic analysis of trapped complexes, the first being that of the trapped fluoroglycosyl-enzyme intermediate of Cex. The crystal structure of the trapped fluorocellobiosyl-enzyme complex for Cex has provided useful insights into catalysis and the roles of specific residues at the active site. In addition, information about the conformation of the natural sugar in the covalently bound state and the interactions at the active site was obtained using a mutant form of Cex.
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Affiliation(s)
- Jacqueline Wicki
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z1
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38
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LIU CHENJIAN, SUZUKI TOHRU, HIRATA SATORU, KAWAI KEIICHI. The Processing of High-Molecular-Weight Xylanase (XynE, 110 kDa) from Aeromonas caviae ME-1 to 60-kDa Xylanase (XynE60) in Escherichia coli and Purification and Characterization of XynE60. J Biosci Bioeng 2003. [DOI: 10.1263/jbb.95.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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39
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Liu CJ, Suzuki T, Hirata S, Kawai K. The processing of high-molecular-weight xylanase (XynE, 110 kDa) fromAeromonas caviae ME-1 to 60-kDa xylanase (XynE60) inEscherichia coli and purification and characterization of XynE60. J Biosci Bioeng 2003; 95:95-101. [PMID: 16233373 DOI: 10.1016/s1389-1723(03)80155-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2002] [Accepted: 09/30/2002] [Indexed: 10/27/2022]
Abstract
A xylanase gene (xynE) encoding XynE (110 kDa) was cloned from a lambda phage genomic library of Aeromonas caviae ME-1 which is a multiple-xylanase-producing bacterium. Upon nucleotide sequence analysis, we found that xynE comprises 2823 by and encodes a protein of 941 amino acid residues (104,153 Da), which was similar to endo-beta-1,4-xylanases which are categorized to glycosyl hydrolase family 10. An Escherichia coli transformant that harbored pXED30 carrying xynE produced 110-, 84-, 72-, and 66-kDa xylanases in the cell-free extract, and 72- and 66-kDa xylanases in the culture supernatant. We purified the 66-kDa xylanase to electrophoretic homogeneity from a culture supernatant by a series of column chromatographies. The calculated molecular mass of the purified xylanase determined by matrix assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was 60,154.50 Da, and the xylanase was designated XynE60. Analysis of the N-terminal 10 amino acid residues and the determined molecular mass of XynE60 revealed that XynE60 is a product processed at the Gly26-Gly27, and Thr565-Ala566 sites of XynE by proteolytic cleavage. XynE60 showed optimal activity at 55 degrees C and pH 8.0, and was stable below 45 degrees C and at pH 7.0-8.5. The K(m) and V(max) of XynE60 were calculated to be 8.1 mg/ml and 6897 nkat/mg, respectively.
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Affiliation(s)
- Chen Jian Liu
- United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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40
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Ly HD, Lougheed B, Wakarchuk WW, Withers SG. Mechanistic studies of a retaining alpha-galactosyltransferase from Neisseria meningitidis. Biochemistry 2002; 41:5075-85. [PMID: 11955055 DOI: 10.1021/bi012031s] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipopolysaccharyl alpha-galactosyltransferase from Neisseria meningitidis catalyzes the transfer of a galactosyl moiety from the activated donor UDP-Gal to glycoconjugates to yield an elongated saccharide product with net retention of anomeric configuration relative to the donor substrate. Through kinetic analyses in which the concentrations of both substrates are independently varied and through inhibition studies with dead-end analogues of both substrates and with the oligosaccharide product, we have demonstrated that this enzyme follows an ordered bi-bi kinetic mechanism. Various aspects of the chemical mechanism including the possible formation of a covalent glycosyl-enzyme intermediate were also probed using an assortment of strategies. While the results of these investigations were unable to clearly delineate the chemical mechanism of this enzyme, they provide important insights into the catalytic machinery surrounding the events involved in catalysis.
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Affiliation(s)
- Hoa D Ly
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T 1Z1 Canada
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41
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Blanchard JE, Gal L, He S, Foisy J, Warren RA, Withers SG. The identification of the catalytic nucleophiles of two beta-galactosidases from glycoside hydrolase family 35. Carbohydr Res 2001; 333:7-17. [PMID: 11423106 DOI: 10.1016/s0008-6215(01)00108-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The beta-galactosidases from Xanthomonas manihotis (beta-Gal Xmn) and Bacillus circulans (beta-Gal-3 Bcir) are retaining glycosidases that hydrolyze glycosidic bonds through a double displacement mechanism involving a covalent glycosyl-enzyme intermediate. The mechanism-based inactivator 2,4-dinitrophenyl 2-deoxy-2-fluoro-beta-D-galactopyranoside was shown to inactivate beta-Gal Xmn and beta-Gal-3 Bcir through the accumulation of 2-deoxy-2-fluorogalactosyl enzyme intermediates with half lives of 40 and 625 h, respectively. Peptic digestion of these labeled enzymes and analysis by LC-MS identified Glu(260) and Glu(233) as the catalytic nucleophiles involved in the formation of the glycosyl-enzyme intermediate during catalysis by beta-Gal Xmn and beta-Gal-3 Bcir, respectively. These findings confirm the previous prediction of the position of these residues based on primary sequence similarities to other members of the glycoside hydrolase family 35.
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Affiliation(s)
- J E Blanchard
- Department of Chemistry, Protein Engineering Network of Centres of Excellence of Canada, University of British Columbia, Vancouver, BC, Canada V6T 1Z1
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42
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Ly HD, Howard S, Shum K, He S, Zhu A, Withers SG. The synthesis, testing and use of 5-fluoro-alpha-D-galactosyl fluoride to trap an intermediate on green coffee bean alpha-galactosidase and identify the catalytic nucleophile. Carbohydr Res 2000; 329:539-47. [PMID: 11128583 DOI: 10.1016/s0008-6215(00)00214-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
5-Fluoro-alpha-D-galactopyranosyl fluoride was synthesized and its interaction with the active site of an alpha-galactosidase from green coffee bean (Coffea arabica), a retaining glycosidase, characterized kinetically and structurally. The compound behaves as an apparently tight binding (Ki = 600 nM) competitive inhibitor, achieving this high affinity through reaction as a slow substrate that accumulates a high steady-state concentration of the glycosyl-enzyme intermediate, as evidenced by ESiMS. Proteolysis of the trapped enzyme coupled with HPLC/MS analysis allowed the localization of a labeled peptide that was subsequently sequenced. Comparison of this sequence information to that of other members of the same glycosidase family revealed the active site nucleophile to be Asp145 within the sequence LKYDNCNNN. The importance of this residue to catalysis has been confirmed by mutagenesis studies.
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Affiliation(s)
- H D Ly
- Department of Chemistry, University of British Columbia, Vancouver, BC, Canada
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43
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Leggio LL, Jenkins J, Harris GW, Pickersgill RW. X-ray crystallographic study of xylopentaose binding to Pseudomonas fluorescens xylanase A. Proteins 2000; 41:362-73. [PMID: 11025547 DOI: 10.1002/1097-0134(20001115)41:3<362::aid-prot80>3.0.co;2-n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The structure of the complex between a catalytically compromised family 10 xylanase and a xylopentaose substrate has been determined by X-ray crystallography and refined to 3.2 A resolution. The substrate binds at the C-terminal end of the eightfold betaalpha-barrel of Pseudomonas fluorescens subsp. cellulosa xylanase A and occupies substrate binding subsites -1 to +4. Crystal contacts are shown to prevent the expected mode of binding from subsite -2 to +3, because of steric hindrance to subsite -2. The loss of accessible surface at individual subsites on binding of xylopentaose parallels well previously reported experimental measurements of individual subsites binding energies, decreasing going from subsite +2 to +4. Nine conserved residues contribute to subsite -1, including three tryptophan residues forming an aromatic cage around the xylosyl residue at this subsite. One of these, Trp 313, is the single residue contributing most lost accessible surface to subsite -1, and goes from a highly mobile to a well-defined conformation on binding of the substrate. A comparison of xylanase A with C. fimi CEX around the +1 subsite suggests that a flatter and less polar surface is responsible for the better catalytic properties of CEX on aryl substrates. The view of catalysis that emerges from combining this with previously published work is the following: (1) xylan is recognized and bound by the xylanase as a left-handed threefold helix; (2) the xylosyl residue at subsite -1 is distorted and pulled down toward the catalytic residues, and the glycosidic bond is strained and broken to form the enzyme-substrate covalent intermediate; (3) the intermediate is attacked by an activated water molecule, following the classic retaining glycosyl hydrolase mechanism.
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Affiliation(s)
- L L Leggio
- Centre for Crystallographic Studies, Chemical Institute, University of Copenhagen, Copenhagen, Denmark.
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44
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Mande SS, Gupta N, Ghosh A, Mande SC. Homology model of a novel xylanase: molecular basis for high-thermostability and alkaline stability. J Biomol Struct Dyn 2000; 18:137-44. [PMID: 11021658 DOI: 10.1080/07391102.2000.10506653] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Xylanases form enzymes of considerable interest to a variety of biotechnological industries. Their industrial usage is especially attractive since they can replace some of the environmental pollutants, and are economically viable. Those with higher thermostability and optimal activity at alkaline pH are of particular importance to the paper and pulp industry due to the demands of conditions under which the enzymatic reactions are carried out. We have earlier isolated a xylanase from Bacillus sp. NG-27, which is active both at high temperature as well as at alkaline pH. In order to find out factors responsible for the adaptation of this enzyme to the extreme conditions, three dimensional structure of NG-27 xylanase has now been obtained by homology modelling. The tertiary structure shows TIM barrel fold consisting of 8 parallel beta-strands surrounded by alpha-helices. The active site is located at the carboxy terminal end of the TIM barrel. Factors which contribute to the thermostability of the enzyme are increased number of salt bridges. The salt bridges occur remarkably on one face of alpha-helices, with oppositely charged residues occupying i, i+4, i+7 positions. A solvent shielded salt bridge interaction is also observed, which is absent in the mesophilic homologous xylanases. Solvent shielding may enhance electrostatic interaction through lowering of the dielectric, and contribute to increased stability of the enzyme.
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Affiliation(s)
- S S Mande
- Institute of Microbial Technology, Chandigarh, India
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45
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Abstract
Enzymatic hydrolysis of glycosides can occur by one of two elementary mechanisms identified by the stereochemical outcome of the reaction, inversion or retention. The key active-site residues involved are a pair of carboxylic acids in each case, and strategies for their identification and for probing the details of their roles in catalysis have been developed through detailed kinetic analysis of mutants. Similarly the roles of other active-site residues have also been probed this way, and mutants have been developed that trap intermediates in catalysis, allowing the determination of the three-dimensional structures of several such key species. By manipulating the locations or even the presence of these carboxyl side chains in the active site, the mechanisms of several glycosidases have been completely changed, and this has allowed the development of "glycosynthases," mutant glycosidases that are capable of synthesizing oligosaccharides but unable to degrade them. Surprisingly little progress has been made on altering specificities through mutagenesis, although recent results suggest that gene shuffling coupled with effective screens will provide the most effective approach.
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Affiliation(s)
- H D Ly
- Department of Chemistry, University of British Columbia, Vancouver, Canada
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46
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Fujimoto Z, Kuno A, Kaneko S, Yoshida S, Kobayashi H, Kusakabe I, Mizuno H. Crystal structure of Streptomyces olivaceoviridis E-86 beta-xylanase containing xylan-binding domain. J Mol Biol 2000; 300:575-85. [PMID: 10884353 DOI: 10.1006/jmbi.2000.3877] [Citation(s) in RCA: 91] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Xylanases hydrolyse the beta-1,4-glycosidic bonds within the xylan backbone and belong to either family 10 or 11 of the glycoside hydrolases, on the basis of the amino acid sequence similarities of their catalytic domains. Generally, xylanases have a core catalytic domain, an N and/or C-terminal substrate-binding domain and a linker region. Until now, X-ray structural analyses of family 10 xylanases have been reported only for their catalytic domains and do not contain substrate-binding domains. We have determined the crystal structure of a family 10 xylanase containing the xylan-binding domain (XBD) from Streptomyces olivaceoviridis E-86 at 1.9 A resolution. The catalytic domain comprises a (beta/alpha)(8)-barrel topologically identical to other family 10 xylanases. XBD has three similar subdomains, as suggested from a triple-repeat sequence, which are assembled against one another around a pseudo-3-fold axis, forming a galactose-binding lectin fold similar to ricin B-chain. The Gly/Pro-rich linker region connecting the catalytic domain and XBD is not visible in the electron density map, probably because of its flexibility. The interface of the two domains in the crystal is hydrophilic, where five direct hydrogen bonds and water-mediated hydrogen bonds exist. The sugar-binding residues seen in ricin/lactose complex are spatially conserved among the three subdomains in XBD, suggesting that all of the subdomains in XBD have the capacity to bind sugars. The flexible linker region enables the two domains to move independently and may provide a triple chance of substrate capturing and catalysis. The structure reported here represents an example where the metabolic enzyme uses a ricin-type lectin motif for capturing the insoluble substrate and promoting catalysis.
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Affiliation(s)
- Z Fujimoto
- Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, IIbaraki, 305-8602, Japan.
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47
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Gupta N, Reddy VS, Maiti S, Ghosh A. Cloning, expression, and sequence analysis of the gene encoding the alkali-stable, thermostable endoxylanase from alkalophilic, mesophilic Bacillus sp. Strain NG-27. Appl Environ Microbiol 2000; 66:2631-5. [PMID: 10831448 PMCID: PMC110591 DOI: 10.1128/aem.66.6.2631-2635.2000] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Alkalophilic Bacillus sp. strain NG-27 produces a 42-kDa endoxylanase active at 70 degrees C and at a pH of 8.4. The gene for this endoxylanase was cloned and sequenced. The gene contained one open reading frame of 1,215 bases. An active site characteristic of the family 10 beta-glycanases was recognized between amino acids 303 and 313, with the active glutamate at position 310. Though highly thermostable, the enzyme contains no cysteine residue.
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Affiliation(s)
- N Gupta
- Institute of Microbial Technology, Sector 39-A, Chandigarh-160036, India
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48
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Hehre EJ. A fresh understanding of the stereochemical behavior of glycosylases: structural distinction of "inverting" (2-MCO-type) versus "retaining" (1-MCO-type) enzymes. Adv Carbohydr Chem Biochem 2000; 55:265-310. [PMID: 10715782 DOI: 10.1016/s0065-2318(00)55007-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- E J Hehre
- Department of Microbiology and Immmunology, Albert Einstein College of Medicine, New York, USA
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49
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Abstract
The cyanogenic glycosides belong to the products of secondary metabolism, to the natural products of plants. These compounds are composed of an alpha-hydroxynitrile type aglycone and of a sugar moiety (mostly D-glucose). The distribution of the cyanogenic glycosides (CGs) in the plant kingdom is relatively wide, the number of CG-containing taxa is at least 2500, and a lot of such taxa belong to families Fabaceae, Rosaceae, Linaceae, Compositae and others. Different methods of determination are discussed (including the indirect classical photometrical and the new direct chromatographic ones). The genetic control of cyanogenesis has no unique mechanism, the plants show variation in the amount of the produced HCN. The production of HCN depends on both the biosynthesis of CGs and on the existence (or absence) of its degrading enzymes. The biosynthetic precursors of the CGs are different L-amino acids, these are hydroxylated then the N-hydroxylamino acids are converted to aldoximes, these are turned into nitriles. The last ones are hydroxylated to alpha-hydroxynitriles and then they are glycosilated to CGs. The generation of HCN from CGs is a two step process involving a deglycosilation and a cleavage of the molecule (regulated by beta-glucosidase and alpha-hydroxynitrilase). The tissue level compartmentalisation of CGs and their hydrolysing enzymes prevents large-scale hydrolysis in intact plant tissue. The actual level of CGs is determined by various factors both developmental and ecological ones, which are reviewed too. The last part of the present work demonstrates the biological roles of CGs in plant physiological processes and in plant defence mechanisms as well. The effect of CGs (HCN) on different animals, the symptoms of poisonings are discussed to cows, sheep, donkeys, horses and chicks. Finally, the poisonous effects of cassava (Manihot esculenta) roots are summarised on experimental animals and on the human organism.
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Affiliation(s)
- J Vetter
- Department of Botany, University of Veterinary Sciences, Budapest, Hungary
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50
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Roldán-Arjona T, Pérez-Espinosa A, Ruiz-Rubio M. Tomatinase from Fusarium oxysporum f. sp. lycopersici defines a new class of saponinases. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 1999; 12:852-61. [PMID: 10517025 DOI: 10.1094/mpmi.1999.12.10.852] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Plants produce a variety of secondary metabolites, many of which have antifungal activity. Saponins are plant glycosides that may provide a preformed chemical barrier against phytopathogenic fungi. Fusarium oxysporum f. sp. lycopersici and other tomato pathogens produce extracellular enzymes known as tomatinases, which deglycosylate alpha-tomatine to yield less toxic derivatives. We have cloned and characterized the cDNA and genomic DNA encoding tomatinase from the vascular pathogen of tomato F. oxysporum f. sp. lycopersici. This gene encodes a protein (FoTom1) with no amino acid sequence homology to any previously described saponinase, including tomatinase from Septoria lycopersici. Although FoTom1 is related to family 10 glycosyl hydrolases, which include mainly xylanases, it has no detectable xylanase activity. We have overexpressed and purified the protein with a bacterial heterologous system. The purified enzyme is active and cleaves alpha-tomatine into the less toxic compounds tomatidine and lycotetraose. Tomatinase from F. oxysporum f. sp. lycopersici is encoded by a single gene whose expression is induced by alpha-tomatine. This expression is fully repressed in the presence of glucose, which is consistent with the presence of two putative CREA binding sites in the promoter region of the tomatinase gene. The tomatinase gene is expressed in planta in both roots and stems throughout the entire disease cycle of F. oxysporum f. sp. lycopersici.
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Affiliation(s)
- T Roldán-Arjona
- Departamento de Genética, Facultad de Ciencias, Universidad de Córdoba, Spain
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