1
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Nagata S, Tomida H, Iwai-Hirose H, Tanaka HN, Ando H, Imamura A, Ishida H. Synthesis of a 1,2- cis-indoxyl galactoside as a chromogenic glycosidase substrate. RSC Adv 2019; 9:28241-28247. [PMID: 35530445 PMCID: PMC9071174 DOI: 10.1039/c9ra05797h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 09/03/2019] [Indexed: 11/24/2022] Open
Abstract
A synthetically challenging 1,2-cis-indoxyl galactoside, X-α-galactoside, was first prepared in this study using a cyclic ketone indoxyl acceptor and a glycosyl trichloroacetimidate donor to produce an enol glycoside and a 4,6-O-di-tert-butylsilylene-protected galactosyl donor to complete the synthesis. The target compound shows enzyme activity in the presence of α-galactosidase. The highly challenging synthesis of a 1,2-cis-indoxyl galactoside was first achieved.![]()
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Affiliation(s)
- Sakuto Nagata
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Hirotaka Tomida
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
| | - Haruka Iwai-Hirose
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
- The United Graduate School of Agricultural Science
| | - Hide-Nori Tanaka
- The United Graduate School of Agricultural Science
- Gifu University
- Gifu 501-1193
- Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
| | - Hiromune Ando
- The United Graduate School of Agricultural Science
- Gifu University
- Gifu 501-1193
- Japan
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN)
| | - Akihiro Imamura
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
- The United Graduate School of Agricultural Science
| | - Hideharu Ishida
- Department of Applied Bioorganic Chemistry
- Gifu University
- Gifu 501-1193
- Japan
- The United Graduate School of Agricultural Science
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2
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Dahbi S, Jacquinet JC, Bertin-Jung I, Robert A, Ramalanjaona N, Gulberti S, Fournel-Gigleux S, Lopin-Bon C. Synthesis of a library of variously modified 4-methylumbelliferyl xylosides and a structure-activity study of human β4GalT7. Org Biomol Chem 2017; 15:9653-9669. [PMID: 29116283 DOI: 10.1039/c7ob02530k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Proteoglycans (PGs) are complex macromolecules that are composed of glycosaminoglycan (GAG) chains covalently attached to a core protein through a tetrasaccharide linker. The biosynthesis of PGs is complex and involves a large number of glycosyltranferases. Here we present a structure-activity study of human β4GalT7, which transfers the first Gal residue onto a xyloside moiety of the linkage region. An efficient and regiocontrolled synthesis of a library of modified analogs of 4-methylumbelliferyl xyloside (XylMU) is reported herein. Hydroxyl groups at the position C-2, C-3 or C-4 have been epimerized and/or replaced by a hydrogen or a fluorine, while the anomeric oxygen was replaced by either a sulfur or a sulfone. The effect of these compounds on human β4GalT7 activity in vitro and on GAG biosynthesis in cellulo was then evaluated.
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Affiliation(s)
- Samir Dahbi
- Univ. Orléans et CNRS, ICOA, UMR 7311, F-45067 Orléans, France.
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3
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Böttcher S, Thiem J. Synthesis of Indoxyl-glycosides for Detection of Glycosidase Activities. J Vis Exp 2015:e52442. [PMID: 26068577 DOI: 10.3791/52442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Indoxyl glycosides proved to be valuable and versatile tools for monitoring glycosidase activities. Indoxyls are released by enzymatic hydrolysis and are rapidly oxidized, for example by atmospheric oxygen, to indigo type dyes. This reaction enables fast and easy screening in vivo without isolation or purification of enzymes, as well as rapid tests on agar plates or in solution (e.g., blue-white screening, micro-wells) and is used in biochemistry, histochemistry, bacteriology and molecular biology. Unfortunately the synthesis of such substrates proved to be difficult, due to various side reactions and the low reactivity of the indoxyl hydroxyl function. Especially for glucose type structures low yields were observed. Our novel approach employs indoxylic acid ester as key intermediates. Indoxylic acid esters with varied substitution patterns were prepared on scalable pathways. Phase transfer glycosylations with those acceptors and peracetylated glycosyl halides can be performed under common conditions in high yields. Ester cleavage and subsequent mild silver mediated glycosylation yields the peracetylated indoxyl glycosides in high yields. Finally deprotection is performed according to Zemplén.
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Affiliation(s)
- Stephan Böttcher
- Department of Chemistry, Faculty of Sciences, University of Hamburg
| | - Joachim Thiem
- Department of Chemistry, Faculty of Sciences, University of Hamburg;
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4
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Brusa C, Muzard M, Rémond C, Plantier-Royon R. β-Xylopyranosides: synthesis and applications. RSC Adv 2015. [DOI: 10.1039/c5ra14023d] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In recent years, β-xylopyranosides have attracted interest due to the development of biomass-derived molecules. This review focuses on general routes for the preparation of β-xylopyranosides by chemical and enzymatic pathways and their main uses.
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Affiliation(s)
- Charlotte Brusa
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
| | - Murielle Muzard
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
| | - Caroline Rémond
- Université de Reims Champagne-Ardenne
- UMR 614
- Fractionnement des AgroRessources et Environnement
- France
- INRA
| | - Richard Plantier-Royon
- Université de Reims Champagne-Ardenne
- Institut de Chimie Moléculaire de Reims (ICMR)
- CNRS UMR 7312
- UFR Sciences Exactes et Naturelles
- F-51687 Reims Cedex 2
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5
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Böttcher S, Thiem J. Indoxylic Acid Esters as Convenient Intermediates Towards Indoxyl Glycosides. European J Org Chem 2013. [DOI: 10.1002/ejoc.201301198] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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6
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Böttcher S, Hederos M, Champion E, Dékány G, Thiem J. Novel efficient routes to indoxyl glycosides for monitoring glycosidase activities. Org Lett 2013; 15:3766-9. [PMID: 23829284 DOI: 10.1021/ol401710a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new efficient synthesis for broad access to indoxyl glycosides was developed. Indoxylic acid allyl ester linked to a sugar structure served as the key intermediate in this route. Selective ester cleavage and mild decarboxylation led to the corresponding indoxyl glycosides in good yields. This synthesis was applied for preparation of indoxyl glycosides of fucose, sialic acid, and 6'-sialyl lactose.
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Affiliation(s)
- Stephan Böttcher
- University of Hamburg , Faculty of Science, Department of Chemistry, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
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7
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Suzuki R, Fujimoto Z, Ito S, Kawahara SI, Kaneko S, Taira K, Hasegawa T, Kuno A. Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86. J Biochem 2009; 146:61-70. [PMID: 19279191 DOI: 10.1093/jb/mvp047] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Retaining glycosyl hydrolases, which catalyse both glycosylation and deglycosylation in a concerted manner, are the most abundant hydrolases. To date, their visualization has tended to be focused on glycosylation because glycosylation reactions can be visualized by inactivating deglycosylation step and/or using substrate analogues to isolate covalent intermediates. Furthermore, during structural analyses of glycosyl hydrolases with hydrolytic reaction products by the conventional soaking method, mutarotation of an anomeric carbon in the reaction products promptly and certainly occurs. This undesirable structural alteration hinders visualization of the second step in the reaction. Here, we investigated X-ray crystallographic visualization as a possible method for visualizing the conformational itinerary of a retaining xylanase from Streptomyces olivaceoviridis E-86. To clearly define the stereochemistry at the anomeric carbon during the deglycosylation step, extraneous nucleophiles, such as azide, were adopted to substitute for the missing base catalyst in an appropriate mutant. The X-ray crystallographic visualization provided snapshots of the components of the entire reaction, including the E*S complex, the covalent intermediate, breakdown of the intermediate and the enzyme-product (E*P)complex.
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Affiliation(s)
- Ryuichiro Suzuki
- Department of Material and Biological Chemistry, Yamagata University, Japan
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8
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Vrsanská M, Nerinckx W, Claeyssens M, Biely P. An alternative approach for the synthesis of fluorogenic substrates of endo-beta-(1-->4)-xylanases and some applications. Carbohydr Res 2007; 343:541-8. [PMID: 18062947 DOI: 10.1016/j.carres.2007.11.011] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/09/2007] [Accepted: 11/09/2007] [Indexed: 11/16/2022]
Abstract
Fluorogenic substrates of endo-beta-(1-->4)-xylanases (EXs), 4-methylumbelliferyl beta-glycosides of xylobiose and xylotriose were synthesized from fully acetylated oligosaccharides using the alpha-trichloroacetimidate procedure. A commercially available syrup containing xylose and xylo-oligosaccharides was used as the starting material. Both fluorogenic glycosides were found to be suitable substrates for EXs, particularly for sensitive detection of the enzymes in electrophoretic gels and their in situ localization on sections of fruiting bodies of some plants, such as tomato, potato and eggplant, all of the family Solanaceae.
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Affiliation(s)
- Mária Vrsanská
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, SK-84538 Bratislava, Slovakia
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9
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Eneyskaya EV, Ivanen DR, Shabalin KA, Kulminskaya AA, Backinowsky LV, Brumer Iii H, Neustroev KN. Chemo-enzymatic synthesis of 4-methylumbelliferyl β-(1→4)-d-xylooligosides: new substrates for β-d-xylanase assays. Org Biomol Chem 2005; 3:146-51. [PMID: 15602610 DOI: 10.1039/b409583a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transglycosylation catalyzed by a beta-D-xylosidase from Aspergillus sp. was used to synthesize a set of 4-methylumbelliferyl (MU) beta-1-->4-D-xylooligosides having the common structure [beta-D-Xyl-(1-->4)]2-5-beta-D-Xyl-MU. MU xylobioside synthesized chemically by the condensation of protected MU beta-D-xylopyranoside with ethyl 2,3,4-tri-O-acetyl-1-thio-beta-D-xylopyranoside was used as a substrate for transglycosylation with the beta-D-xylosidase from Aspergillus sp. to produce higher MU xylooligosides. The structures of oligosaccharides obtained were established by 1H and 13C NMR spectroscopy and electrospray tandem mass spectrometry. MU beta-D-xylooligosides synthesized were tested as fluorogenic substrates for the GH-10 family beta-D-xylanase from Aspergillus orizae and the GH-11 family beta-D-xylanase I from Trichoderma reesei. Both xylanases released the aglycone from MU xylobioside and the corresponding trioside. With substrates having d.p. 4 and 5, the enzymes manifested endolytic activities, splitting off MU, MUX, and MUX2 primarily.
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Affiliation(s)
- Elena V Eneyskaya
- Petersburg Nuclear Physics Institute, Russian Academy of Science, Molecular and Radiation Biology Division, Gatchina, 188300, Russia
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10
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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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11
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Borriss R, Krah M, Brumer H, Kerzhner MA, Ivanen DR, Eneyskaya EV, Elyakova LA, Shishlyannikov SM, Shabalin KA, Neustroev KN. Enzymatic synthesis of 4-methylumbelliferyl (1-->3)-beta-D-glucooligosaccharides-new substrates for beta-1,3-1,4-D-glucanase. Carbohydr Res 2003; 338:1455-67. [PMID: 12829391 DOI: 10.1016/s0008-6215(03)00199-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The transglycosylation reactions catalyzed by beta-1,3-D-glucanases (laminaranases) were used to synthesize a number of 4-methylumbelliferyl (MeUmb) (1-->3)-beta-D-gluco-oligosaccharides having the common structure [beta-D-Glcp-(1-->3)](n)-beta-D-Glcp-MeUmb, where n=1-5. The beta-1,3-D-glucanases used were purified from the culture liquid of Oerskovia sp. and from a homogenate of the marine mollusc Spisula sachalinensis. Laminaran and curdlan were used as (1-->3)-beta-D-glucan donor substrates, while MeUmb-beta-D-glucoside (MeUmbGlcp) was employed as a transglycosylation acceptor. Modification of [beta-D-Glcp-(1-->3)](2)-beta-D-Glcp-MeUmb (MeUmbG(3)) gives 4,6-O-benzylidene-D-glucopyranosyl or 4,6-O-ethylidene-D-glucopyranosyl groups at the non-reducing end of artificial oligosaccharides. The structures of all oligosaccharides obtained were solved by 1H and 13C NMR spectroscopy and electrospray tandem mass spectrometry. The synthetic oligosaccharides were shown to be substrates for a beta-1,3-1,4-D-glucanase from Rhodothermus marinus, which releases MeUmb from beta-di- and beta-triglucosides and from acetal-protected beta-triglucosides. When acting upon substrates with d.p.>3, the enzyme exhibits an endolytic activity, primarily cleaving off MeUmbGlcp and MeUmbG(2).
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Affiliation(s)
- Rainer Borriss
- AG Bakteriengenetik, Institut fur Biologie, Humboldt Universität Berlin Chausseestrasse 117, D-10115 Berlin, Germany
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12
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Nishimoto M, Honda Y, Kitaoka M, Hayashi K. A kinetic study on pH-activity relationship of XynA from alkaliphilic Bacillus halodurans C-125 using aryl-xylobiosides. J Biosci Bioeng 2002; 93:428-30. [PMID: 16233226 DOI: 10.1016/s1389-1723(02)80079-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2001] [Accepted: 12/27/2001] [Indexed: 10/27/2022]
Abstract
Xylanase A from alkaliphilic Bacillus halodurans C-125 was expressed in Escherichia coli and purified by affinity and anion exchange chromatographies. It exhibited a strong substrate inhibition using xylan as the substrate. Its K(i) value increased with an increase in pH. The effect of pH on the enzyme activity was determined using two aryl-xylobiosides as substrates, and it was found that the enzyme had a flat k(cat)-pH curve in the pH range of 5.8-8.8. This range was different from that obtained with 0.45% xylan as previously reported (Honda, H. et al., Agric. Biol. Chem., 49, 3165-3169, 1985). The substrate inhibition was presumed to cause the difference. It has been clarified that the use of aryl-xylobiosides as substrates yields more accurate kinetic results than that of xylan.
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Affiliation(s)
- Mamoru Nishimoto
- Enzyme Laboratory, National Food Research Institute, Kannondai, Ibaraki 305-8642, Japan
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13
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Honda Y, Kitaoka M, Sakka K, Ohmiya K, Hayashi K. An investigation of the pH-activity relationships of Cex, a family 10 xylanase from Cellulomonas fimi: xylan inhibition and the influence of nitro-substituted aryl-β-d-xylobiosides on xylanase activity. J Biosci Bioeng 2002. [DOI: 10.1016/s1389-1723(02)80034-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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14
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Kuno A, Kaneko S, Ohtsuki H, Ito S, Fujimoto Z, Mizuno H, Hasegawa T, Taira K, Kusakabe I, Hayashi K. Novel sugar-binding specificity of the type XIII xylan-binding domain of a family F/10 xylanase from Streptomyces olivaceoviridis E-86. FEBS Lett 2000; 482:231-6. [PMID: 11024466 DOI: 10.1016/s0014-5793(00)02067-6] [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: 10/18/2022]
Abstract
The type XIII xylan-binding domain (XBD) of a family F/10 xylanase (FXYN) from Streptomyces olivaceoviridis E-86 was found to be structurally similar to the ricin B chain which recognizes the non-reducing end of galactose and specifically binds to galactose containing sugars. The crystal structure of XBD [Fujimoto, Z. et al. (2000) J. Mol. Biol. 300, 575-585] indicated that the whole structure of XBD is very similar to the ricin B chain and the amino acids which form the galactose-binding sites are highly conserved between the XBD and the ricin B chain. However, our investigation of the binding abilities of wt FXYN and its truncated mutants towards xylan demonstrated that the XBD bound xylose-based polysaccharides. Moreover, it was found that the sugar-binding unit of the XBD was a trimer, which was demonstrated in a releasing assay using sugar ranging in size from xylose to xyloheptaose. These results indicated that the binding specificity of the XBD was different from those of the same family lectins such as the ricin B chain. Somewhat surprisingly, it was found that lactose could release the XBD from insoluble xylan to a level half of that observed for xylobiose, indicating that the XBD also possessed the same galactose recognition site as the ricin B chain. It appears that the sugar-binding pocket of the XBD has evolved from the ancient ricin super family lectins to bind additional sugar targets, resulting in the differences observed in the sugar-binding specificities between the lectin group (containing the ricin B chain) and the enzyme group.
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Affiliation(s)
- A Kuno
- Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.
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