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Suzuki R, Fujimoto Z, Kaneko S, Hasegawa T, Kuno A. Enhanced Azidolysis by the Formation of Stable Ser-His Catalytic Dyad in a Glycoside Hydrolase Family 10 Xylanase Mutant. J Appl Glycosci (1999) 2018; 65:1-8. [PMID: 34354506 PMCID: PMC8056907 DOI: 10.5458/jag.jag.jag-2017_011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 11/04/2022] Open
Abstract
Glycoside hydrolases require carboxyl groups as catalysts for their activity. A retaining xylanase from Streptomyces olivaceoviridis E-86 belonging to glycoside hydrolase family 10 possesses Glu128 and Glu236 that respectively function as acid/base and nucleophile. We previously developed a unique mutant of the retaining xylanase, N127S/E128H, whose deglycosylation is triggered by azide. A crystallographic study reported that the transient formation of a Ser–His catalytic dyad in the reaction cycle possibly reduced the azidolysis reaction. In the present study, we engineered a catalytic dyad with enhanced stability by site-directed mutagenesis and crystallographic study of N127S/E128H. Comparison of the Michaelis complexes of N127S/E128H with pNP-X2 and with xylopentaose showed that Ser127 could form an alternative hydrogen bond with Thr82, which disrupts the formation of the Ser–His catalytic dyad. The introduction of T82A mutation in N127S/E128H produces an enhanced first-order rate constant (6 times that of N127S/E128H). We confirmed the presence of a stable Ser–His hydrogen bond in the Michaelis complex of the triple mutant, which forms the productive tautomer of His128 that acts as an acid catalyst. Because the glycosyl azide is applicable in the bioconjugation of glycans by using click chemistry, the enzyme-assisted production of the glycosyl azide may contribute to the field of glycobiology.
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Affiliation(s)
- Ryuichiro Suzuki
- 1 Department of Biological Production, Akita Prefectural University.,2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Zui Fujimoto
- 3 Advanced Analysis Center, National Agriculture and Food Research Organization (NARO)
| | - Satoshi Kaneko
- 4 Department of Subtropical Biochemistry and Biotechnology, Faculty of Agriculture, University of the Ryukyus
| | - Tsunemi Hasegawa
- 2 Department of Material and Biological Chemistry, Faculty of Science, Yamagata University
| | - Atsushi Kuno
- 5 Biotechnology Research Institute for Drug Discovery (BRD), National Institute of Advanced Industrial Science and Technology (AIST)
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Purification and characterization of a cellulase-free, thermostable endo-xylanase from Streptomyces griseorubens LH-3 and its use in biobleaching on eucalyptus kraft pulp. J Biosci Bioeng 2018; 125:46-51. [DOI: 10.1016/j.jbiosc.2017.08.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/16/2017] [Accepted: 08/11/2017] [Indexed: 11/18/2022]
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Structure and Function of Carbohydrate-Binding Module Families 13 and 42 of Glycoside Hydrolases, Comprising a β-Trefoil Fold. Biosci Biotechnol Biochem 2014; 77:1363-71. [DOI: 10.1271/bbb.130183] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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4
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Maehara T, Fujimoto Z, Ichinose H, Michikawa M, Harazono K, Kaneko S. Crystal structure and characterization of the glycoside hydrolase family 62 α-L-arabinofuranosidase from Streptomyces coelicolor. J Biol Chem 2014; 289:7962-72. [PMID: 24482228 DOI: 10.1074/jbc.m113.540542] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
α-L-arabinofuranosidase, which belongs to the glycoside hydrolase family 62 (GH62), hydrolyzes arabinoxylan but not arabinan or arabinogalactan. The crystal structures of several α-L-arabinofuranosidases have been determined, although the structures, catalytic mechanisms, and substrate specificities of GH62 enzymes remain unclear. To evaluate the substrate specificity of a GH62 enzyme, we determined the crystal structure of α-L-arabinofuranosidase, which comprises a carbohydrate-binding module family 13 domain at its N terminus and a catalytic domain at its C terminus, from Streptomyces coelicolor. The catalytic domain was a five-bladed β-propeller consisting of five radially oriented anti-parallel β-sheets. Sugar complex structures with l-arabinose, xylotriose, and xylohexaose revealed five subsites in the catalytic cleft and an l-arabinose-binding pocket at the bottom of the cleft. The entire structure of this GH62 family enzyme was very similar to that of glycoside hydrolase 43 family enzymes, and the catalytically important acidic residues found in family 43 enzymes were conserved in GH62. Mutagenesis studies revealed that Asp(202) and Glu(361) were catalytic residues, and Trp(270), Tyr(461), and Asn(462) were involved in the substrate-binding site for discriminating the substrate structures. In particular, hydrogen bonding between Asn(462) and xylose at the nonreducing end subsite +2 was important for the higher activity of substituted arabinofuranosyl residues than that for terminal arabinofuranoses.
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Affiliation(s)
- Tomoko Maehara
- From the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642
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Park H, Ahn J, Lee J, Lee H, Kim C, Jung JK, Lee H, Lee EG. Expression, immobilization and enzymatic properties of glutamate decarboxylase fused to a cellulose-binding domain. Int J Mol Sci 2011; 13:358-68. [PMID: 22312257 PMCID: PMC3269691 DOI: 10.3390/ijms13010358] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 12/15/2011] [Accepted: 12/19/2011] [Indexed: 11/24/2022] Open
Abstract
Escherichia coli-derived glutamate decarboxylase (GAD), an enzyme that catalyzes the conversion of glutamic acid to gamma-aminobutyric acid (GABA), was fused to the cellulose-binding domain (CBD) and a linker of Trichoderma harzianum endoglucanase II. To prevent proteolysis of the fusion protein, the native linker was replaced with a S3N10 peptide known to be completely resistant to E. coli endopeptidase. The CBD-GAD expressed in E. coli was successfully immobilized on Avicel, a crystalline cellulose, with binding capacity of 33 ± 2 nmolCBD-GAD/gAvicel and the immobilized enzymes retained 60% of their initial activities after 10 uses. The results of this report provide a feasible alternative to produce GABA using immobilized GAD through fusion to CBD.
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Affiliation(s)
- Hyemin Park
- Biotechnology Process Engineering Center, KRIBB, Daejeon 305-600, Korea; E-Mails: (H.P.); (J.A.); (J.L.); (H.L.); (C.K.); (J.-K.J.); (H.L.)
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Ichinose H, Fujimoto Z, Honda M, Harazono K, Nishimoto Y, Uzura A, Kaneko S. A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27. J Biol Chem 2009; 284:25097-106. [PMID: 19608743 PMCID: PMC2757213 DOI: 10.1074/jbc.m109.022723] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 07/01/2009] [Indexed: 11/06/2022] Open
Abstract
Arabinogalactan proteins (AGPs) are a family of plant cell surface proteoglycans and are considered to be involved in plant growth and development. Because AGPs are very complex molecules, glycoside hydrolases capable of degrading AGPs are powerful tools for analyses of the AGPs. We previously reported such enzymes from Streptomyces avermitilis. Recently, a beta-l-arabinopyranosidase was purified from the culture supernatant of the bacterium, and its corresponding gene was identified. The primary structure of the protein revealed that the catalytic module was highly similar to that of glycoside hydrolase family 27 (GH27) alpha-d-galactosidases. The recombinant protein was successfully expressed as a secreted 64-kDa protein using a Streptomyces expression system. The specific activity toward p-nitrophenyl-beta-l-arabinopyranoside was 18 micromol of arabinose/min/mg, which was 67 times higher than that toward p- nitrophenyl-alpha-d-galactopyranoside. The enzyme could remove 0.1 and 45% l-arabinose from gum arabic or larch arabinogalactan, respectively. X-ray crystallographic analysis reveals that the protein had a GH27 catalytic domain, an antiparallel beta-domain containing Greek key motifs, another antiparallel beta-domain forming a jellyroll structure, and a carbohydrate-binding module family 13 domain. Comparison of the structure of this protein with that of alpha-d-galactosidase showed a single amino acid substitution (aspartic acid to glutamic acid) in the catalytic pocket of beta-l-arabinopyranosidase, and a space for the hydroxymethyl group on the C-5 carbon of d-galactose bound to alpha-galactosidase was changed in beta-l-arabinopyranosidase. Mutagenesis study revealed that the residue is critical for modulating the enzyme activity. This is the first report in which beta-l-arabinopyranosidase is classified as a new member of the GH27 family.
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Affiliation(s)
- Hitomi Ichinose
- From the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642
| | - Zui Fujimoto
- the Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, and
| | - Mariko Honda
- From the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642
| | - Koichi Harazono
- the Research & Development Center, Nagase & Company, Limited, 2-2-3 Murotani, Nishi-Ku, Kobe, Hyogo 651-2241, Japan
| | - Yukifumi Nishimoto
- the Research & Development Center, Nagase & Company, Limited, 2-2-3 Murotani, Nishi-Ku, Kobe, Hyogo 651-2241, Japan
| | - Atsuko Uzura
- the Research & Development Center, Nagase & Company, Limited, 2-2-3 Murotani, Nishi-Ku, Kobe, Hyogo 651-2241, Japan
| | - Satoshi Kaneko
- From the Food Biotechnology Division, National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642
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Fujimoto Z, Ichinose H, Harazono K, Honda M, Uzura A, Kaneko S. Crystallization and preliminary crystallographic analysis of beta-L-arabinopyranosidase from Streptomyces avermitilis NBRC14893. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:632-4. [PMID: 19478450 DOI: 10.1107/s1744309109017230] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 05/07/2009] [Indexed: 11/10/2022]
Abstract
Beta-L-arabinopyranosidase from Streptomyces avermitilis NBRC14893 is a monomeric protein consisting of a catalytic domain belonging to glycosyl hydrolase family 27, an unknown domain and a substrate-binding domain belonging to carbohydrate-binding module family 13. The complete enzyme (residues 45-658) has successfully been cloned and homologously expressed in the Streptomyces expression system. beta-L-Arabinopyranosidase was crystallized by the sitting-drop vapour-diffusion method. The crystals diffracted to 1.6 A resolution and belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 68.2, b = 98.9, c = 181.3 A. The Matthews coefficient was calculated to be 2.38 A(3) Da(-1).
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Affiliation(s)
- Zui Fujimoto
- Protein Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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Mchunu NP, Singh S, Permaul K. Expression of an alkalo-tolerant fungal xylanase enhanced by directed evolution in Pichia pastoris and Escherichia coli. J Biotechnol 2009; 141:26-30. [DOI: 10.1016/j.jbiotec.2009.02.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Revised: 02/20/2009] [Accepted: 02/26/2009] [Indexed: 12/19/2022]
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Iwaki J, Minamisawa T, Tateno H, Kominami J, Suzuki K, Nishi N, Nakamura T, Hirabayashi J. Desulfated galactosaminoglycans are potential ligands for galectins: evidence from frontal affinity chromatography. Biochem Biophys Res Commun 2008; 373:206-12. [PMID: 18555795 DOI: 10.1016/j.bbrc.2008.05.190] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2008] [Accepted: 05/30/2008] [Indexed: 11/24/2022]
Abstract
Galectins, a group of beta-galactoside-binding lectins, are involved in multiple functions through specific binding to their oligosaccharide ligands. No previous work has focused on their interaction with glycosaminoglycans (GAGs). In the present work, affinities of established members of human galectins toward a series of GAGs were investigated, using frontal affinity chromatography. Structurally-defined keratan sulfate (KS) oligosaccharides showed significant affinity to a wide range of galectins if Gal residue(s) remained unsulfated, while GlcNAc sulfation had relatively little effect. Consistently, galectins showed much higher affinity to corneal type I than cartilageous type II KS. Unexpectedly, galectin-3, -7, and -9 also exerted significant affinity to desulfated, GalNAc-containing GAGs, i.e., chondroitin and dermatan, but not at all to hyaluronan and N-acetylheparosan. These observations revealed that the integrity of 6-OH of betaGalNAc is important for galectin recognition of these galactosaminoglycans, which were shown, for the first time, to be implicated as potential ligands of galectins.
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Affiliation(s)
- Jun Iwaki
- Lectin Application and Analysis Team, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
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Purification of the alkaliphilic xylanases from Myceliophthora sp. IMI 387099 using cellulose-binding domain as an affinity tag. World J Microbiol Biotechnol 2007. [DOI: 10.1007/s11274-007-9561-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Ichinose H, Kuno A, Kotake T, Yoshida M, Sakka K, Hirabayashi J, Tsumuraya Y, Kaneko S. Characterization of an exo-beta-1,3-galactanase from Clostridium thermocellum. Appl Environ Microbiol 2006; 72:3515-23. [PMID: 16672498 PMCID: PMC1472343 DOI: 10.1128/aem.72.5.3515-3523.2006] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A gene encoding an exo-beta-1,3-galactanase from Clostridium thermocellum, Ct1,3Gal43A, was isolated. The sequence has similarity with an exo-beta-1,3-galactanase of Phanerochaete chrysosporium (Pc1,3Gal43A). The gene encodes a modular protein consisting of an N-terminal glycoside hydrolase family 43 (GH43) module, a family 13 carbohydrate-binding module (CBM13), and a C-terminal dockerin domain. The gene corresponding to the GH43 module was expressed in Escherichia coli, and the gene product was characterized. The recombinant enzyme shows optimal activity at pH 6.0 and 50 degrees C and catalyzes hydrolysis only of beta-1,3-linked galactosyl oligosaccharides and polysaccharides. High-performance liquid chromatography analysis of the hydrolysis products demonstrated that the enzyme produces galactose from beta-1,3-galactan in an exo-acting manner. When the enzyme acted on arabinogalactan proteins (AGPs), the enzyme produced oligosaccharides together with galactose, suggesting that the enzyme is able to accommodate a beta-1,6-linked galactosyl side chain. The substrate specificity of the enzyme is very similar to that of Pc1,3Gal43A, suggesting that the enzyme is an exo-beta-1,3-galactanase. Affinity gel electrophoresis of the C-terminal CBM13 did not show any affinity for polysaccharides, including beta-1,3-galactan. However, frontal affinity chromatography for the CBM13 indicated that the CBM13 specifically interacts with oligosaccharides containing a beta-1,3-galactobiose, beta-1,4-galactosyl glucose, or beta-1,4-galactosyl N-acetylglucosaminide moiety at the nonreducing end. Interestingly, CBM13 in the C terminus of Ct1,3Gal43A appeared to interfere with the enzyme activity toward beta-1,3-galactan and alpha-l-arabinofuranosidase-treated AGP.
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Affiliation(s)
- Hitomi Ichinose
- National Food Research Institute, 2-1-12 Kannondai, Tsukuba, Ibaraki 305-8642, Japan
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Hemmi H, Kuno A, Ito S, Suzuki R, Kaneko S, Hasegawa T, Hirabayashi J, Kasai KI. (1)H, (13)C, and (15)N chemical shift assignment of the C-terminal 15 kDa domain of a novel galactose-binding protein from the earthworm Lumbricus terrestris. JOURNAL OF BIOMOLECULAR NMR 2004; 30:377-378. [PMID: 15756471 DOI: 10.1007/s10858-005-1845-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Accepted: 07/20/2004] [Indexed: 05/24/2023]
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