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Sekiya H, Nonaka Y, Kamitori S, Miyaji T, Tamai E. X-ray structure and mutagenesis analyses of Clostridioides difficile endolysin Ecd09610 glucosaminidase domain. Biochem Biophys Res Commun 2024; 715:149957. [PMID: 38688057 DOI: 10.1016/j.bbrc.2024.149957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/15/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Clostridioides difficile endolysin (Ecd09610) consists of an unknown domain at its N terminus, followed by two catalytic domains, a glucosaminidase domain and endopeptidase domain. X-ray structure and mutagenesis analyses of the Ecd09610 catalytic domain with glucosaminidase activity (Ecd09610CD53) were performed. Ecd09610CD53 was found to possess an α-bundle-like structure with nine helices, which is well conserved among GH73 family enzymes. The mutagenesis analysis based on X-ray structures showed that Glu405 and Asn470 were essential for enzymatic activity. Ecd09610CD53 may adopt a neighboring-group mechanism for a catalytic reaction in which Glu405 acted as an acid/base catalyst and Asn470 helped to stabilize the oxazolinium ion intermediate. Structural comparisons with the newly identified Clostridium perfringens autolysin catalytic domain (AcpCD) in the P1 form and a zymography analysis demonstrated that AcpCD was 15-fold more active than Ecd09610CD53. The strength of the glucosaminidase activity of the GH73 family appears to be dependent on the depth of the substrate-binding groove.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Yasuhiro Nonaka
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Shigehiro Kamitori
- Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan; Research Facility Center for Science & Technology, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Tomomi Miyaji
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan.
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2
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Kamitori S. X-ray structures of Enterobacter cloacae allose-binding protein in complexes with monosaccharides demonstrate its unique recognition mechanism for high affinity to allose. Biochem Biophys Res Commun 2023; 682:187-192. [PMID: 37820454 DOI: 10.1016/j.bbrc.2023.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 10/03/2023] [Indexed: 10/13/2023]
Abstract
d-Allose is an aldohexose of the C3-epimer of d-glucose, existing in very small amounts in nature, called a rare sugar. The operon responsible for d-allose metabolism, the allose operon, was found in several bacteria, which consists of seven genes: alsR, alsB, alsA, alsC, alsE, alsK, and rpiB. To understand the biological implication of the allose operon utilizing a rare sugar of d-allose as a carbon source, it is important to clarify whether the allose operon functions specifically for d-allose or also functions for other ligands. It was proposed that the allose operon can function for d-ribose, which is essential as a component of nucleotides and abundant in nature. Allose-binding protein, AlsB, coded in the allose operon, is thought to capture a ligand outside the cell, and is expected to show high affinity for the specific ligand. X-ray structure determinations of Enterobacter cloacae AlsB (EtcAlsB) in ligand-free form, and in complexes with d-allose, d-ribose, and d-allulose, and measurements of the thermal parameters of the complex formation using an isothermal titration calorimeter were performed. The results demonstrated that EtcAlsB has a unique recognition mechanism for high affinity to d-allose by changing its conformation from an open to a closed form depending on d-allose-binding, and that the binding of d-ribose to EtcAlsB could not induce a completely closed form but an intermediate form, explaining the low affinity for d-ribose.
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Affiliation(s)
- Shigehiro Kamitori
- Research Facility Center for Science & Technology and Faculty of Medicine, International Institute of Rare Sugar Research and Education, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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3
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Tamai E, Yamada M, Ishida T, Arimura N, Matsunami R, Sekiya H, Kamitori S. Structural and biochemical characterization of Clostridium perfringens pili protein B collagen-binding domains. FEBS Lett 2023; 597:1345-1354. [PMID: 37071018 DOI: 10.1002/1873-3468.14626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/17/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023]
Abstract
Sortase-mediated pili are flexible rod proteins composed of major and minor/tip pilins, playing important roles in the initial adhesion of bacterial cells to host tissues. The pilus shaft is formed by covalent polymerization of major pilins, and the minor/tip pilin is covalently attached to the tip of the shaft involved in adhesion to the host cell. The Gram-positive bacterium Clostridium perfringens has a major pilin, and a minor/tip pilin (CppB) with the collagen-binding motif. Here, we report X-ray structures of CppB collagen-binding domains, collagen-binding assays, and mutagenesis analysis, demonstrating that CppB collagen-binding domains adopt an L-shaped structure in open form, and that a small β-sheet unique to CppB provides a scaffold for a favorable binding site for collagen peptide.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Mitsugu Yamada
- Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba, Ibaraki, 305-8505, Japan
| | - Takuya Ishida
- Japan Aerospace Exploration Agency (JAXA), 2-1-1 Sengen, Tsukuba, Ibaraki, 305-8505, Japan
| | - Nayu Arimura
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Risa Matsunami
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Shigehiro Kamitori
- Research Facility Center for Science & Technology and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
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Sekiya H, Kobayashi S, Takahashi I, Kamitori S, Tamai E. Biochemical Characterizations of the Putative Amidase Endolysin Ecd18980 Catalytic Domain from Clostridioides difficile. Biol Pharm Bull 2023; 46:1625-1629. [PMID: 37914365 DOI: 10.1248/bpb.b23-00265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Clostridioides difficile is the major causative pathogen of pseudomembranous colitis, and novel antimicrobial agents are required for treatment. Phage-derived endolysins exhibiting species-specific lytic activity have potential as novel antimicrobial agents. We surveyed the genome of C. difficile strain 630 and identified a gene encoding an endolysin, Ecd18980, which has an amidase_3 domain at the N-terminus but unknown C-terminal domain. The genes encoding Ecd18980 and its catalytic domain (Ecd18980CD) were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. These purified proteins showed lytic activity against C. difficile. Ecd18980CD showed higher lytic activity than the wild-type enzyme and near-specific lytic activity against C. difficile. This species specificity is thought to depend on substrate cleavage activity rather than binding. We also characterized the biochemical properties of Ecd18980CD, including optimal pH, salt concentration, and thermal stability.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University
| | - Saki Kobayashi
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University
| | - Ikumi Takahashi
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University
| | - Shigehiro Kamitori
- Research Facility Center for Science and Technology, Faculty of Medicine, Kagawa University
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University
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5
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Nonaka Y, Ogawa T, Shoji H, Nishi N, Kamitori S, Nakamura T. Crystal structure and conformational stability of a galectin-1 tandem-repeat mutant with a short linker. Glycobiology 2021; 32:251-259. [PMID: 34735570 DOI: 10.1093/glycob/cwab101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 11/14/2022] Open
Abstract
Modification of the domain architecture of galectins has been attempted to analyze their biological functions and to develop medical applications. Several types of galectin-1 repeat mutants were previously reported but, however, it was not clear whether the native structure of the wild type was retained. In this study, we determined the crystal structure of a galectin-1 tandem-repeat mutant with a short linker peptide, and compared the unfolding profiles of the wild type and mutant by chemical denaturation. The structure of the mutant was consistent with that of the dimer of the wild type, and both carbohydrate-binding sites were retained. The unfolding curve of the wild type with lactose suggested that the dimer dissociation and the tertiary structure unfolding was concomitant at micromolar protein concentrations. The midpoint denaturant concentration of the wild type was dependent on the protein concentration and lower than that of the mutant. Linking the two subunits significantly stabilized the tertiary structure. The mutant exhibited higher T-cell growth-inhibition activity and comparable hemagglutinating activity. Structural stabilization may prevent the oxidation of the internal cysteine residue.
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Affiliation(s)
- Yasuhiro Nonaka
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Takashi Ogawa
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Hiroki Shoji
- Department of Biology, Kanazawa Medical University, 1-1 Daigaku, Uchinada, Kahoku, Ishikawa 920-0293, Japan
| | - Nozomu Nishi
- Life Science Research Center, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Shigehiro Kamitori
- Life Science Research Center, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Takanori Nakamura
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Sekiya H, Kamitori S, Nariya H, Matsunami R, Tamai E. Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+-dependent amidase endolysin, Psa, catalytic domain. Biochem Biophys Res Commun 2021; 576:66-72. [PMID: 34482025 DOI: 10.1016/j.bbrc.2021.08.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022]
Abstract
Phage-derived endolysins, enzymes that degrade peptidoglycans, have the potential to serve as alternative antimicrobial agents. Psa, which was identified as an endolysin encoded in the genome of Clostridium perfringens st13, was shown to specifically lyse C. perfringens. Psa has an N-terminal catalytic domain that is homologous to the Amidase_2 domain (PF01510), and a novel C-terminal cell wall-binding domain. Here, we determined the X-ray structure of the Psa catalytic domain (Psa-CD) at 1.65 Å resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central β-sheet surrounded by two α-helix groups. Furthermore, there is a Zn2+ at the center of Psa-CD catalytic reaction site, as well as a unique T-shaped substrate-binding groove consisting of two grooves on the molecule surface. We performed modeling study of the enzyme/substrate complex along with a mutational analysis, and demonstrated that the structure of the substrate-binding groove is closely related to the amidase activity. Furthermore, we proposed a Zn2+-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology, Graduate School of Human Life Sciences Food and Nutritional Sciences, Jumonji University, 2-1-28, Kansawa, Niiza, Saitama, 352-8510, Japan
| | - Risa Matsunami
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan; Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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7
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Nonaka Y, Ogawa T, Shoji H, Nishi N, Kamitori S, Nakamura T. Modulation of the carbohydrate-binding specificity of two Xenopus proto-type galectins by site-directed mutagenesis. Biochim Biophys Acta Proteins Proteom 2021; 1869:140684. [PMID: 34146732 DOI: 10.1016/j.bbapap.2021.140684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/29/2022]
Abstract
The galectin family is a representative soluble lectin group, which is responsible for the modulation of various cell functions. Although the carbohydrate-binding specificity of galectins has been well-studied, the relationship between protein structure and specificity remains to be elucidated. We previously reported the characteristics of a Xenopus laevis skin galectin, xgalectin-Va, which had diverged from galectin-1. The carbohydrate selectivity of xgalectin-Va was different from that of human galectin-1 and xgalectin-Ib (a Xenopus laevis galectin-1 homolog). In this study, we clarified the key residues for this selectivity by site-directed mutagenesis. Substitution of two amino acids of xgalectin-Va, Val56Gly/Lys76Arg, greatly enhanced the binding ability to N-acetyllactosamine and conferred significant T-cell growth inhibition activity, although the wild type had no activity. These two residues, Gly54 and Arg74 in galectin-1, would cooperatively contribute to the N-acetyllactosamine recognition. The loop region between the S4 and S5 β-strands was involved in the binding to the TF-antigen disaccharide. The loop substitution successfully changed the carbohydrate selectivity of xgalectin-Va and xgalectin-Ib.
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Affiliation(s)
- Yasuhiro Nonaka
- Department of Endocrinology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Takashi Ogawa
- Department of Endocrinology, Faculty of Medicine, Kagawa University, Kagawa, Japan
| | - Hiroki Shoji
- Department of Biology, Kanazawa Medical University, Ishikawa, Japan
| | - Nozomu Nishi
- Life Science Research Center, Kagawa University, Kagawa, Japan
| | | | - Takanori Nakamura
- Department of Endocrinology, Faculty of Medicine, Kagawa University, Kagawa, Japan.
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8
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Yoshida H, Yoshihara A, Kato S, Mochizuki S, Akimitsu K, Izumori K, Kamitori S. Crystal structure of a novel homodimeric l-ribulose 3-epimerase from Methylomonus sp. FEBS Open Bio 2021; 11:1621-1637. [PMID: 33838083 PMCID: PMC8167858 DOI: 10.1002/2211-5463.13159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 01/07/2023] Open
Abstract
d-Allulose has potential as a low-calorie sweetener which can suppress fat accumulation. Several enzymes capable of d-allulose production have been isolated, including d-tagatose 3-epimerases. Here, we report the isolation of a novel protein from Methylomonas sp. expected to be a putative enzyme based on sequence similarity to ketose 3-epimerase. The synthesized gene encoding the deduced ketose 3-epimerase was expressed as a recombinant enzyme in Escherichia coli, and it exhibited the highest enzymatic activity toward l-ribulose, followed by d-ribulose and d-allulose. The X-ray structure analysis of l-ribulose 3-epimerase from Methylomonas sp. (MetLRE) revealed a homodimeric enzyme, the first reported structure of dimeric l-ribulose 3-epimerase. The monomeric structure of MetLRE is similar to that of homotetrameric l-ribulose 3-epimerases, but the short C-terminal α-helix of MetLRE is unique and different from those of known l-ribulose 3 epimerases. The length of the C-terminal α-helix was thought to be involved in tetramerization and increasing stability; however, the addition of residues to MetLRE at the C terminus did not lead to tetramer formation. MetLRE is the first dimeric l-ribulose 3-epimerase identified to exhibit high relative activity toward d-allulose.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of MedicineKagawa UniversityKitaJapan,International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan
| | - Akihide Yoshihara
- International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan,Faculty of AgricultureKagawa UniversityKitaJapan
| | - Shiro Kato
- International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan,Faculty of AgricultureKagawa UniversityKitaJapan
| | - Susumu Mochizuki
- International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan,Faculty of AgricultureKagawa UniversityKitaJapan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan,Faculty of AgricultureKagawa UniversityKitaJapan
| | - Ken Izumori
- International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan,Faculty of AgricultureKagawa UniversityKitaJapan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of MedicineKagawa UniversityKitaJapan,International Institute of Rare Sugar Research and EducationKagawa UniversityKitaJapan
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Tamai E, Sekiya H, Nariya H, Katayama S, Kamitori S. X-ray structures of Clostridium perfringens sortase C with C-terminal cell wall sorting motif of LPST demonstrate role of subsite for substrate-binding and structural variations of catalytic site. Biochem Biophys Res Commun 2021; 554:138-144. [PMID: 33794418 DOI: 10.1016/j.bbrc.2021.03.106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 03/19/2021] [Indexed: 11/30/2022]
Abstract
Pili of Gram-positive bacteria are flexible rod proteins covalently attached to the bacterial cell wall, that play important roles in the initial adhesion of bacterial cells to host tissues and bacterial colonization. Pili are formed by the polymerization of major and minor pilins, catalyzed by class C sortase (SrtC), a family of cysteine transpeptidases. The Gram-positive bacterium Clostridium perfringens has a major pilin (CppA), a minor pilin (CppB), and SrtC (CpSrtC). CpSrtC recognizes the C-terminal cell wall sorting signal motifs with five amino acid residues, LPSTG of CppA and LPETG of CppB, for the polymerization of pili. Here, we report biochemical analysis to detect the formation of Clostridium perfringens pili in vivo, and the X-ray structure of a novel intermolecular substrate-enzyme complex of CpSrtC with a sequence of LPST at the C-terminal site. The results showed that CpSrtC has a subsite for substrate-binding to aid polymerization of pili, and that the catalytic site has structural variations, giving insights into the enzyme catalytic reaction mechanism and affinities for the C-terminal cell wall sorting signal motif sequences.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan; Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology, Graduate School of Human Life Sciences Food and Nutritional Sciences, Jumonji University, 2-1-28, Kansawa, Niiza, Saitama, 352-8510, Japan
| | - Seiichi Katayama
- Department of Life Science, Faculty of Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama, 700-0005, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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10
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Sekiya H, Tamai E, Kawasaki J, Murakami K, Kamitori S. Structural and biochemical characterizations of the novel autolysin Acd24020 from Clostridioides difficile and its full-function catalytic domain as a lytic enzyme. Mol Microbiol 2020; 115:684-698. [PMID: 33140473 DOI: 10.1111/mmi.14636] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 10/13/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022]
Abstract
Autolysin is a lytic enzyme that hydrolyzes peptidoglycans of the bacterial cell wall, with a catalytic domain and cell wall-binding (CWB) domains, to be involved in different physiological functions that require bacterial cell wall remodeling. We identified a novel autolysin, Acd24020, from Clostridioides (Clostridium) difficile (C. difficile), with an endopeptidase catalytic domain belonging to the NlpC/P60 family and three bacterial Src-homology 3 domains as CWB domains. The catalytic domain of Acd24020 (Acd24020-CD) exhibited C. difficile-specific lytic activity equivalent to Acd24020, indicating that Acd24020-CD has full-function as a lytic enzyme by itself. To elucidate the specific peptidoglycan-recognition and catalytic reaction mechanisms of Acd24020-CD, biochemical characterization, X-ray structure determination, a modeling study of the enzyme/substrate complex, and mutagenesis analysis were performed. Acd24020-CD has an hourglass-shaped substrate-binding groove across the molecule, which is responsible for recognizing the direct 3-4 cross-linking structure unique to C. difficile peptidoglycan. Based on the X-ray structure and modeling study, we propose a dynamic Cys/His catalyzing mechanism, in which the catalytic Cys299 and His354 residues dynamically change their conformations to complement each step of the enzyme catalytic reaction.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
| | - Jurina Kawasaki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Kaho Murakami
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Matsuyama, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Japan
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Itoh A, Nonaka Y, Nakakita SI, Yoshida H, Nishi N, Nakamura T, Kamitori S. Structures of human galectin-10/monosaccharide complexes demonstrate potential of monosaccharides as effectors in forming Charcot-Leyden crystals. Biochem Biophys Res Commun 2020; 525:S0006-291X(20)30303-X. [PMID: 32081418 DOI: 10.1016/j.bbrc.2020.02.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/06/2020] [Indexed: 10/25/2022]
Abstract
The galectins are a family of β-galactoside-specific animal lectins, and have attracted much attention as novel regulators of the immune system. Galectin-10 is well-expressed in eosinophils, and spontaneously forms Charcot-Leyden crystals (CLCs), during prolonged eosinophilic inflammatory reactions, which are frequently observed in eosinophilic diseases. Although biochemical and structural characterizations of galectin-10 have been done, its biological role and molecular mechanism are still unclear, and few X-ray structures of galectin-10 in complex with monosaccharides/oligosaccharides have been reported. Here, X-ray structures of galectin-10 in complexes with seven monosaccharides are presented with biochemical analyses to detect interactions of galectin-10 with monosaccharides/oligosaccharides. Galectin-10 forms a homo-dimer in the face-to-face orientation, and the monosaccharides bind to the carbohydrate recognition site composed of amino acid residues from two galectin-10 molecules of dimers, suggesting that galectin-10 dimer likely captures the monosaccharides in solution and in vivo. d-Glucose, d-allose, d-arabinose, and D-N-acetylgalactosamine bind to the interfaces between galectin-10 dimers in crystals, and they affect the stability of molecular packing in crystals, leading to easy-dissolving of CLCs, and/or inhibiting the formation of CLCs. These monosaccharides may serve as effectors of G10 to form CLCs in vivo.
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Affiliation(s)
- Aiko Itoh
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Yasuhiro Nonaka
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan; Departments of Endocrinology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Shin-Ichi Nakakita
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Nozomu Nishi
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Takanori Nakamura
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan; Departments of Endocrinology, Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kagawa, Japan.
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Yoshida H, Kojima K, Shiota M, Yoshimatsu K, Yamazaki T, Ferri S, Tsugawa W, Kamitori S, Sode K. X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein. Acta Crystallogr D Struct Biol 2019; 75:841-851. [PMID: 31478907 PMCID: PMC6719666 DOI: 10.1107/s2059798319010878] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022]
Abstract
The X-ray structure of the catalytic subunit of Burkholderia cepacia FAD glucose dehydrogenase complexed with a hitchhiker protein was determined as a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. The 3Fe–4S cluster is present at the surface of the catalytic subunit and serves in the intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The bacterial flavin adenine dinucleotide (FAD)-dependent glucose dehydrogenase complex derived from Burkholderia cepacia (BcGDH) is a representative molecule of direct electron transfer-type FAD-dependent dehydrogenase complexes. In this study, the X-ray structure of BcGDHγα, the catalytic subunit (α-subunit) of BcGDH complexed with a hitchhiker protein (γ-subunit), was determined. The most prominent feature of this enzyme is the presence of the 3Fe–4S cluster, which is located at the surface of the catalytic subunit and functions in intramolecular and intermolecular electron transfer from FAD to the electron-transfer subunit. The structure of the complex revealed that these two molecules are connected through disulfide bonds and hydrophobic interactions, and that the formation of disulfide bonds is required to stabilize the catalytic subunit. The structure of the complex revealed the putative position of the electron-transfer subunit. A comparison of the structures of BcGDHγα and membrane-bound fumarate reductases suggested that the whole BcGDH complex, which also includes the membrane-bound β-subunit containing three heme c moieties, may form a similar overall structure to fumarate reductases, thus accomplishing effective electron transfer.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Katsuhiro Kojima
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Masaki Shiota
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Keiichi Yoshimatsu
- Department of Chemistry, Missouri State University, Springfield, MO 65897, USA
| | - Tomohiko Yamazaki
- Research Center for Functional Materials, National Institute for Materials Science (NIMS), 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
| | - Stefano Ferri
- Department of Applied Chemistry and Biochemical Engineering, Shizuoka University, 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
| | - Wakako Tsugawa
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Tamai E, Katayama S, Sekiya H, Nariya H, Kamitori S. Structures of major pilins in Clostridium perfringens demonstrate dynamic conformational change. Acta Crystallogr D Struct Biol 2019; 75:718-732. [PMID: 31373571 DOI: 10.1107/s2059798319009689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]
Abstract
Pili in Gram-positive bacteria are flexible rod proteins associated with the bacterial cell surface, and they play important roles in the initial adhesion to host tissues and colonization. The pilus shaft is formed by the covalent polymerization of major pilins, catalyzed by sortases, a family of cysteine transpeptidases. Here, X-ray structures of the major pilins from Clostridium perfringens strains 13 and SM101 and of sortase from strain SM101 are presented with biochemical analysis to detect the formation of pili in vivo. The major pilin from strain 13 adopts an elongated structure to form noncovalently linked polymeric chains in the crystal, yielding a practical model of the pilus fiber structure. The major pilin from strain SM101 adopts a novel bent structure and associates to form a left-handed twist like an antiparallel double helix in the crystal, which is likely to promote bacterial cell-cell interactions. A modeling study showed that pilin with a bent structure interacts favorably with sortase. The major pilin from strain SM101 was considered to be in an equilibrium state between an elongated and a bent structure through dynamic conformational change, which may be involved in pili-mediated colonization and sortase-mediated polymerization of pili.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Seiichi Katayama
- Department of Life Science, Faculty of Science, Okayama University of Science, 1-1 Ridai-cho, Kita-ku, Okayama 700-0005, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime 790-8578, Japan
| | - Hirofumi Nariya
- Graduate School of Biosphere Science, Hiroshima University, 1-4-4 Kagamiyama-cho, Higashihiroshima, Hiroshima 739-8528, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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14
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Yoshida H, Yoshihara A, Gullapalli PK, Ohtani K, Akimitsu K, Izumori K, Kamitori S. X-ray structure of Arthrobacter globiformis M30 ketose 3-epimerase for the production of D-allulose from D-fructose. Acta Crystallogr F Struct Biol Commun 2018; 74:669-676. [PMID: 30279320 PMCID: PMC6168773 DOI: 10.1107/s2053230x18011706] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 08/19/2018] [Indexed: 12/18/2022] Open
Abstract
The X-ray structure of ketose 3-epimerase from Arthrobacter globiformis M30, which was previously reported to be a D-allulose 3-epimerase (AgD-AE), was determined at 1.96 Å resolution. The crystal belonged to the hexagonal space group P6522, with unit-cell parameters a = b = 103.98, c = 256.53 Å. The structure was solved by molecular replacement using the structure of Mesorhizobium loti L-ribulose 3-epimerase (MlL-RE), which has 41% sequence identity, as a search model. A hexagonal crystal contained two molecules in the asymmetric unit, and AgD-AE formed a homotetramer with twofold symmetry. The overall structure of AgD-AE was more similar to that of MlL-RE than to the known structures of D-psicose (alternative name D-allulose) 3-epimerases (D-PEs or D-AEs), although AgD-AE and MlL-RE have different substrate specificities. Both AgD-AE and MlL-RE have long helices in the C-terminal region that would contribute to the stability of the homotetramer. AgD-AE showed higher enzymatic activity for L-ribulose than D-allulose; however, AgD-AE is stable and is a unique useful enzyme for the production of D-allulose from D-fructose.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
| | - Akihide Yoshihara
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | | | - Kouhei Ohtani
- Matsutani Chemical Industry Co. Ltd, 5-3 Kita-Itami, Itami, Hyogo 664-8508, Japan
| | - Kazuya Akimitsu
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
- Faculty of Agriculture, Kagawa University, 2393 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0795, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- International Institute of Rare Sugar Research and Education, Kagawa University, Kagawa, Japan
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15
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Tonozuka T, Nihira T, Mizuno M, Nishikawa A, Kamitori S. Mutagenesis-induced conformational change in domain B of a pullulan-hydrolyzing α-amylase TVA I. ACTA ACUST UNITED AC 2018. [DOI: 10.1515/amylase-2018-0001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
An α-amylase from Thermoactinomyces vulgaris, TVA I, hydrolyzes both α-1,4- and α-1,6-glucosidic linkages. Two variants of TVA I have been previously constructed, one containing a substitution of three residues, Ala357- Gln359-Tyr360, with Val-Asn-Glu (AQY/VNE), and the other bearing a deletion of 11 residues from Ala363 to Asn373 (Del11). The activities of both AQY/VNE and Del11 for the α-1,4-glucosidic linkage of maltotriose were decreased compared to that of wild-type TVA I, while the activities of the two variants for the α-1,6-glucosidic linkage of a trisaccharide, isopanose, were less significantly altered. Here, we determined the crystal structures of AQY/VNE and Del11. The structure of AQY/VNE was almost isomorphous with that of wild-type TVA I. On the other hand, the structure of Del11 showed that a conformational change in domain B was induced by the 11-residue deletion, causing narrowing of the catalytic cleft. Taken together with the results of kinetic analysis, this narrower catalytic cleft is likely responsible for the preference of the TVA I enzyme for the α-1,6-glucosidic linkage.
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Retnoningrum DS, Yoshida H, Arumsari S, Kamitori S, Ismaya WT. The first crystal structure of manganese superoxide dismutase from the genus Staphylococcus. Acta Crystallogr F Struct Biol Commun 2018; 74:135-142. [PMID: 29497016 PMCID: PMC5947698 DOI: 10.1107/s2053230x18001036] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 01/17/2018] [Indexed: 11/10/2022] Open
Abstract
A recombinant Staphylococcus equorum manganese superoxide dismutase (MnSOD) with an Asp13Arg substitution displays activity over a wide range of pH, at high temperature and in the presence of chaotropic agents, and retains 50% of its activity after irradiation with UVC for up to 45 min. Interestingly, Bacillus subtilis MnSOD does not have the same stability, despite having a closely similar primary structure and thus presumably also tertiary structure. Here, the crystal structure of S. equorum MnSOD at 1.4 Å resolution is reported that may explain these differences. The crystal belonged to space group P3221, with unit-cell parameters a = 57.36, b = 57.36, c = 105.76 Å, and contained one molecule in the asymmetric unit. The symmetry operation indicates that the enzyme has a dimeric structure, as found in nature and in B. subtilis MnSOD. As expected, their overall structures are nearly identical. However, the loop connecting the helical and α/β domains of S. equorum MnSOD is shorter than that in B. subtilis MnSOD, and adopts a conformation that allows more direct water-mediated hydrogen-bond interactions between the amino-acid side chains of the first and last α-helices in the latter domain. Furthermore, S. equorum MnSOD has a slightly larger buried area compared with the dimer surface area than that in B. subtilis MnSOD, while the residues that form the interaction in the dimer-interface region are highly conserved. Thus, the stability of S. equorum MnSOD may not originate from the dimeric form alone. Furthermore, an additional water molecule was found in the active site. This allows an alternative geometry for the coordination of the Mn atom in the active site of the apo form. This is the first structure of MnSOD from the genus Staphylococcus and may provide a template for the structural study of other MnSODs from this genus.
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Affiliation(s)
- Debbie S. Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Sekar Arumsari
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Bandung Institute of Technology, Jalan Ganesa No. 10, Bandung 40132, Indonesia
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Wangsa T. Ismaya
- Dexa Laboratories of Biomolecular Sciences, Jl. Industri Selatan V Blok PP No. 7, Kawasan Industri Jababeka II, Cikarang 17550, Indonesia
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18
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19
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Tamai E, Sekiya H, Maki J, Nariya H, Yoshida H, Kamitori S. X-ray structure of Clostridium perfringens sortase B cysteine transpeptidase. Biochem Biophys Res Commun 2017; 493:1267-1272. [DOI: 10.1016/j.bbrc.2017.09.144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 10/18/2022]
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20
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Yoshida H, Nishi N, Wada K, Nakamura T, Hirashima M, Kuwabara N, Kato R, Kamitori S. X-ray structure of a protease-resistant mutant form of human galectin-9 having two carbohydrate recognition domains with a metal-binding site. Biochem Biophys Res Commun 2017; 490:1287-1293. [PMID: 28687490 DOI: 10.1016/j.bbrc.2017.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 07/03/2017] [Indexed: 11/29/2022]
Abstract
Galectin-9 (G9) is a tandem-repeat type β-galactoside-specific animal lectin having N-terminal and C-terminal carbohydrate recognition domains (N-CRD and C-CRD, respectively) joined by a linker peptide that is involved in the immune system. G9 is divalent in glycan binding, and structural information about the spatial arrangement of the two CRDs is very important for elucidating its biological functions. As G9 is protease sensitive due to the long linker, the protease-resistant mutant form of G9 (G9Null) was developed by modification of the linker peptide, while retaining its biological functions. The X-ray structure of a mutant form of G9Null with the replacement of Arg221 by Ser (G9Null_R221S) having two CRDs was determined. The structure of G9Null_R221S was compact to associate the two CRDs in the back-to-back orientation with a large interface area, including hydrogen bonds and hydrophobic interactions. A metal ion was newly found in the galectin structure, possibly contributing to the stable structure of protein. The presented X-ray structure was thought to be one of the stable structures of G9, which likely occurs in solution. This was supported by structural comparisons with other tandem-repeated galectins and the analyses of protein thermostability by CD spectra measurements.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Nozomu Nishi
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Kenji Wada
- Department of Chemistry for Medicine, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Takanori Nakamura
- Department of Endocrinology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Mitsuomi Hirashima
- Department of Immunology and Immunopathology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Naoyuki Kuwabara
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Ryuichi Kato
- Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan.
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Tamai E, Sekiya H, Goda E, Makihata N, Maki J, Yoshida H, Kamitori S. Structural and biochemical characterization of the Clostridium perfringens autolysin catalytic domain. FEBS Lett 2016; 591:231-239. [PMID: 27926788 DOI: 10.1002/1873-3468.12515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/17/2016] [Accepted: 11/26/2016] [Indexed: 11/08/2022]
Abstract
Bacterial autolysins can partially hydrolyze cell wall peptidoglycans into small sections to regulate cell separation/division and the growth phase. Clostridium perfringens autolysin (Acp) has an N-terminal cell wall-binding domain and a C-terminal catalytic domain with glucosaminidase activity that belongs to the glycoside hydrolase 73 family. Here, we determined the X-ray structure of the Acp catalytic domain (AcpCD) at 1.76 Å resolution. AcpCD has a unique crescent-shaped structure, forming a deep groove for substrate-binding at the center of the protein. The modeling study of the enzyme/substrate complex demonstrated that the length of the substrate-binding groove is closely related to the glucosaminidase activity. Mutagenesis analysis showed that AcpCD likely adopts a neighboring-group mechanism for the catalytic reaction.
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Affiliation(s)
- Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan.,Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Eri Goda
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Nahomi Makihata
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Jun Maki
- Department of Infectious Disease, College of Pharmaceutical Science, Matsuyama University, Bunkyo-cho, Ehime, Japan
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
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Kobayashi J, Yoshida H, Yagi T, Kamitori S, Hayashi H, Mizutani K, Takahashi N, Mikami B. Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti. J Biosci Bioeng 2016; 123:154-162. [PMID: 27568368 DOI: 10.1016/j.jbiosc.2016.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 11/27/2022]
Abstract
The flavoenzyme 2-Methyl-3-hydroxypyridine-5-carboxylic acid oxygenase (MHPCO) catalyzes the cleavage of the pyridine ring of 2-methyl-3-hydroxypyridine-5-carboxylic acid (MHPC) in the presence of NADH, molecular oxygen, and water. MHPCO also catalyzes the NADH oxidation reaction uncoupled with ring opening in the absence of MHPC (the basal activity). The enzyme shows activity toward not only MHPC but also 5-hydroxynicotinic acid (5HN) and 5-pyridoxic acid (5PA). The reaction rate toward 5PA is extremely low (5% of the activity toward MHPC or 5HN). We determined the crystal structures of MHPCO without substrate and the MHPCO/5HN and MHPCO/5PA complexes, together with a Y270F mutant without substrate and its 5HN complex. The Tyr270 residue was located in the active site and formed hydrogen bonds between the Oη and water molecules to make the active site hydrophilic. Although Tyr270 took a fixed conformation in the structures of the MHPCO and MHPCO/5HN complex, it took two conformations in its 5PA complex, accompanied by two conformations of the bound 5PA. In the wild-type (WT) enzyme, the turnover number of the ring-opening activity was 6800 times that of the basal activity (1300 and 0.19 s-1, respectively), whereas no such difference was observed in the Y270F (19 and 7.4 s-1) or Y270A (0.05 and 0.84 s-1) mutants. In the Y270F/5HN complex, the substrate bound ∼1 Å farther away than in the WT enzyme. These results revealed that Tyr270 is essential to maintain the WT conformation, which in turn enhances the coupling of the NADH oxidation with the ring-opening reaction.
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Affiliation(s)
- Jun Kobayashi
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan.
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kitagun, Kagawa 761-0793, Japan
| | - Toshiharu Yagi
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kitagun, Kagawa 761-0793, Japan
| | - Hideyuki Hayashi
- Department of Chemistry, Osaka Medical College, 2-7 Daigaku-cho, Takatsuki 569-8686, Japan
| | - Kimihiko Mizutani
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan
| | - Nobuyuki Takahashi
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan
| | - Bunzo Mikami
- Laboratory of Applied Structural Biology, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji, Kyoto 611-0011, Japan
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Yoshida H, Yoshihara A, Ishii T, Izumori K, Kamitori S. X-ray structures of the Pseudomonas cichorii D-tagatose 3-epimerase mutant form C66S recognizing deoxy sugars as substrates. Appl Microbiol Biotechnol 2016; 100:10403-10415. [PMID: 27368739 DOI: 10.1007/s00253-016-7673-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Revised: 06/02/2016] [Accepted: 06/08/2016] [Indexed: 12/18/2022]
Abstract
Pseudomonas cichorii D-tagatose 3-epimerase (PcDTE), which has a broad substrate specificity, efficiently catalyzes the epimerization of not only D-tagatose to D-sorbose but also D-fructose to D-psicose (D-allulose) and also recognizes the deoxy sugars as substrates. In an attempt to elucidate the substrate recognition and catalytic reaction mechanisms of PcDTE for deoxy sugars, the X-ray structures of the PcDTE mutant form with the replacement of Cys66 by Ser (PcDTE_C66S) in complexes with deoxy sugars were determined. These X-ray structures showed that substrate recognition by the enzyme at the 1-, 2-, and 3-positions is responsible for enzymatic activity and that substrate-enzyme interactions at the 4-, 5-, and 6-positions are not essential for the catalytic reaction of the enzyme leading to the broad substrate specificity of PcDTE. They also showed that the epimerization site of 1-deoxy 3-keto D-galactitol is shifted from C3 to C4 and that 1-deoxy sugars may bind to the catalytic site in the inhibitor-binding mode. The hydrophobic groove that acts as an accessible surface for substrate binding is formed through the dimerization of PcDTE. In PcDTE_C66S/deoxy sugar complex structures, bound ligand molecules in both the linear and ring forms were detected in the hydrophobic groove, while bound ligand molecules in the catalytic site were in the linear form. This result suggests that the sugar-ring opening of a substrate may occur in the hydrophobic groove and also that the narrow channel of the passageway to the catalytic site allows a substrate in the linear form to pass through.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Kagawa, Japan
| | - Akihide Yoshihara
- Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Tomohiko Ishii
- Faculty of Engineering, Kagawa University, Hayashi-cho, Takamatsu, Kagawa, Japan
| | - Ken Izumori
- Rare Sugar Research Center and Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Kagawa, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Kagawa, Japan.
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Yoshida H, Sakai G, Mori K, Kojima K, Kamitori S, Sode K. Structural analysis of fungus-derived FAD glucose dehydrogenase. Sci Rep 2015; 5:13498. [PMID: 26311535 PMCID: PMC4642536 DOI: 10.1038/srep13498] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/28/2015] [Indexed: 11/29/2022] Open
Abstract
We report the first three-dimensional structure of fungus-derived glucose dehydrogenase using flavin adenine dinucleotide (FAD) as the cofactor. This is currently the most advanced and popular enzyme used in glucose sensor strips manufactured for glycemic control by diabetic patients. We prepared recombinant nonglycosylated FAD-dependent glucose dehydrogenase (FADGDH) derived from Aspergillus flavus (AfGDH) and obtained the X-ray structures of the binary complex of enzyme and reduced FAD at a resolution of 1.78 Å and the ternary complex with reduced FAD and D-glucono-1,5-lactone (LGC) at a resolution of 1.57 Å. The overall structure is similar to that of fungal glucose oxidases (GOxs) reported till date. The ternary complex with reduced FAD and LGC revealed the residues recognizing the substrate. His505 and His548 were subjected for site-directed mutagenesis studies, and these two residues were revealed to form the catalytic pair, as those conserved in GOxs. The absence of residues that recognize the sixth hydroxyl group of the glucose of AfGDH, and the presence of significant cavity around the active site may account for this enzyme activity toward xylose. The structural information will contribute to the further engineering of FADGDH for use in more reliable and economical biosensing technology for diabetes management.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa University, Kagawa 761-0793, Japan
| | - Genki Sakai
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kazushige Mori
- Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan
| | - Katsuhiro Kojima
- Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa University, Kagawa 761-0793, Japan
| | - Koji Sode
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16, Naka-cho, Koganei, Tokyo 184-8588, Japan.,Ultizyme International Ltd., 1-13-16, Minami, Meguro, Tokyo 152-0013, Japan
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Nonaka Y, Ogawa T, Yoshida H, Shoji H, Nishi N, Kamitori S, Nakamura T. Crystal structure of a Xenopus laevis skin proto-type galectin, close to but distinct from galectin-1. Glycobiology 2015; 25:792-803. [DOI: 10.1093/glycob/cwv020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/22/2015] [Indexed: 12/31/2022] Open
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Terami Y, Yoshida H, Uechi K, Morimoto K, Takata G, Kamitori S. Essentiality of tetramer formation of Cellulomonas parahominis L-ribose isomerase involved in novel L-ribose metabolic pathway. Appl Microbiol Biotechnol 2015; 99:6303-13. [DOI: 10.1007/s00253-015-6417-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/15/2015] [Accepted: 01/18/2015] [Indexed: 11/30/2022]
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Terami Y, Yoshida H, Uechi K, Takata G, Kamitori S. Crystal structure of L-ribose isomerase from Cellulomonas parahominis MB426. Acta Crystallogr A Found Adv 2014. [DOI: 10.1107/s2053273314083235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Monosaccharides and their derivatives which hardly exist in nature are so-called "rare sugars". Rare sugars have significance not only in food industries but also pharmaceutical industries. We discovered a novel L-ribose isomerase from Cellulomonas parahominis (CpL-RbI, 249 amino acids), which catalyzes the reversible isomerization between L-ribose and L-ribulose, L-allose and L-psicose, and D-talose and D-tagatose. Since CpL-RbI has a broad substrate specificity, it is useful for the production of various rare sugars. To elucidate the molecular basis of unique enzymatic properties of CpL-RbI, we determined its crystal structure. The N-terminal His-tagged CpL-RbI overexpressed in Escherichia coli was purified using a nickel affinity column. Crystals of CpL-RbI were obtained from a reservoir solution of 0.1 M sodium acetate trihydrate (pH 4.6) with 3.9 M ammonium acetate, by a hanging-drop vapor-diffusion method at 293 K (Space group C2221, a = 76.8, b = 88.6, c = 152.3 Å). X-ray diffraction data were collected up to 2.10 Å resolution using a Rigaku R-AXIS VII on a RA-Micro7HF rotating anode generator (40 kV, 30 mA) at 100 K. The structure was solved by a molecular replacement method with a structure of Acinetobacter sp L-ribose isomerase (4NS7) as a search model, and refined to R-factor of 0.227. CpL-RbI had a cupin-type beta-barrel structure, and the catalytic site was found between two large beta-sheets with a bound metal ion (Fig. 1). There were two protein molecules in an asymmetric unit, forming a homo-dimer with a non-crystallographic 2-fold symmetry (Fig.1). Furthermore, the PISA server showed that two dimers in crystal were associated to form a stable tetramer. Complex structures with substrates, L-ribose, L-allose and L-psicose, were also successfully determined. We will discuss a broad substrate specificity and catalytic reaction mechanism of CpL-RbI based on its three-dimensional structure.
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Yoshida H, Yoshihara A, Teraoka M, Terami Y, Takata G, Izumori K, Kamitori S. X-ray structure of a novell-ribose isomerase acting on a non-natural sugarl-ribose as its ideal substrate. FEBS J 2014; 281:3150-64. [DOI: 10.1111/febs.12850] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/30/2014] [Accepted: 05/15/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
| | | | - Misa Teraoka
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
| | - Yuji Terami
- Rare Sugar Research Center; Kagawa University; Japan
| | - Goro Takata
- Rare Sugar Research Center; Kagawa University; Japan
| | - Ken Izumori
- Rare Sugar Research Center; Kagawa University; Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine; Kagawa University; Japan
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Tamai E, Yoshida H, Sekiya H, Nariya H, Miyata S, Okabe A, Kuwahara T, Maki J, Kamitori S. X-ray structure of a novel endolysin encoded by episomal phage phiSM101 ofClostridium perfringens. Mol Microbiol 2014; 92:326-37. [DOI: 10.1111/mmi.12559] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2014] [Indexed: 12/01/2022]
Affiliation(s)
- Eiji Tamai
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hiromi Yoshida
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Hiroshi Sekiya
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Hirofumi Nariya
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Shigeru Miyata
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
- College of Bioscience and Biotechnology; Chubu University; 1200 Matsumoto-cho Kasugai Aichi 487-8501 Japan
| | - Akinobu Okabe
- Department of Human Nutrition; Faculty of Contemporary Life Science; Chugokugakuen University; Niwase 83 Kita-ku Okayama 761-0197 Japan
| | - Tomomi Kuwahara
- Department of Microbiology; Faculty of Medicine; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
| | - Jun Maki
- Department of Infectious Disease; College of Pharmaceutical Science; Matsuyama University; 4-2 Bunkyo-cho Matsuyama Ehime 790-8578 Japan
| | - Shigehiro Kamitori
- Life Science Research Center; Kagawa University; 1750-1, Ikenobe, Miki-cho Kita-gun Kagawa 761-0793 Japan
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30
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Iwasa C, Tonozuka T, Shinoda M, Sagane Y, Niwa K, Watanabe T, Yoshida H, Kamitori S, Takao T, Oguma K, Nishikawa A. Purification, crystallization and preliminary X-ray analysis of an HA17-HA70 (HA2-HA3) complex from Clostridium botulinum type C progenitor toxin. Acta Crystallogr F Struct Biol Commun 2013; 70:64-7. [PMID: 24419620 DOI: 10.1107/s2053230x13032378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
The haemagglutinin (HA) complex of Clostridium botulinum type C toxin is composed of three types of subcomponents: HA33, HA17 and HA70 (also known as HA1, HA2 and HA3, respectively). Here, a 260 kDa HA17-HA70 complex was crystallized. His-tagged HA17 and maltose-binding-protein-tagged HA70 were expressed in Escherichia coli and their complex was affinity-purified using a combination of amylose resin chromatography and nickel-nitrilotriacetic acid agarose chromatography. Diffraction data were collected to 8.0 Å resolution and the crystal belonged to the tetragonal space group P4(1)2(1)2. The molecular-replacement solution indicated that one molecule of HA17 was bound to each HA70 monomer.
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Affiliation(s)
- Chikako Iwasa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Takashi Tonozuka
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Masaya Shinoda
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yoshimasa Sagane
- Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Koichi Niwa
- Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Toshihiro Watanabe
- Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493, Japan
| | - Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Toshifumi Takao
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiji Oguma
- Asahi Medical College Group, 1-40 Ezu-cho, Kita-ku, Okayama 700-0028, Japan
| | - Atsushi Nishikawa
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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31
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Asahina Y, Kamitori S, Takao T, Nishi N, Hojo H. Chemoenzymatic Synthesis of the Immunoglobulin Domain of Tim-3 Carrying a Complex-Type N-Glycan by Using a One-pot Ligation. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303073] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Asahina Y, Kamitori S, Takao T, Nishi N, Hojo H. Chemoenzymatic Synthesis of the Immunoglobulin Domain of Tim-3 Carrying a Complex-Type N-Glycan by Using a One-pot Ligation. Angew Chem Int Ed Engl 2013; 52:9733-7. [DOI: 10.1002/anie.201303073] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/29/2013] [Indexed: 01/05/2023]
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33
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Nonaka Y, Ogawa T, Oomizu S, Nakakita SI, Nishi N, Kamitori S, Hirashima M, Nakamura T. Self-association of the galectin-9 C-terminal domain via the opposite surface of the sugar-binding site. J Biochem 2013; 153:463-71. [PMID: 23389308 DOI: 10.1093/jb/mvt009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Galectin-9 is a lectin, which has various biological functions such as T-cell differentiation and apoptosis. Multivalency of carbohydrate binding is required for galectin-9 to function. Although galectin-1 (a proto-type galectin) forms an oligomer to obtain its multivalency, galectin-9 (a tandem-repeat-type one) has two carbohydrate recognition domains (CRD) in one polypeptide. However, a single CRD of galectin-9, especially the C-terminal one, exhibited pro-apoptotic activity suggesting oligomer formation capability. In this study, we monitored the nuclear magnetic resonance (NMR) signals of the backbone atoms of the galectin-9 C-terminal CRD (G9CCRD). Protein concentration dependence of the signals suggested that a region (F1-F4 strands) opposite to the ligand-binding site was involved in the self-association of G9CCRD. Site-directed mutagenesis in this region (Leu210, Trp277 and Leu279 to Thr; G9CCRD-3T) inhibited the self-association of G9CCRD, and improved the solubility, whereas it reduced its pro-apoptotic activity towards T cells. The high pro-apoptotic activity of G9CCRD seems to be due to the ability to form an oligomer. In addition, the same substitution in two-CRD-containing galectin-9 (G9Null-3T) also diminished the self-association and improved its solubility, although it hardly reduced the anti-proliferative and pro-apoptotic activities. G9CCRD contributes the self-association of full-length galectin-9 at high protein concentrations.
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Affiliation(s)
- Yasuhiro Nonaka
- Department of Endocrinology, Kagawa University, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Yoshida H, Yoshihara A, Teraoka M, Yamashita S, Izumori K, Kamitori S. Structure of l-rhamnose isomerase in complex with l-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site. FEBS Open Bio 2012; 3:35-40. [PMID: 23772372 PMCID: PMC3668531 DOI: 10.1016/j.fob.2012.11.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Accepted: 11/30/2012] [Indexed: 11/26/2022] Open
Abstract
l-Rhamnose isomerase (l-RhI) catalyzes the reversible isomerization of l-rhamnose to l-rhamnulose. Previously determined X-ray structures of l-RhI showed a hydride-shift mechanism for the isomerization of substrates in a linear form, but the mechanism for opening of the sugar-ring is still unclear. To elucidate this mechanism, we determined X-ray structures of a mutant l-RhI in complex with l-rhamnopyranose and d-allopyranose. Results suggest that a catalytic water molecule, which acts as an acid/base catalyst in the isomerization reaction, is likely to be involved in pyranose-ring opening, and that a newly found substrate sub-binding site in the vicinity of the catalytic site may recognize different anomers of substrates.
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Key Words
- D327N, mutant P. stutzeril-RhI, with a substitution of Asp327 with Asn
- E. coli, Escherichia coli
- H101N, mutant P. stutzeril-RhI, with a substitution of H101 with Asn
- P. stutzeri, Pseudomonas stutzeri
- Pseudomonas stutzeri
- RNS, l-rhamnose in a linear form
- Rare sugar
- Sugar-ring opening mechanism
- X-ray structure
- l-RhI, l-rhamnose isomerase
- l-Rhamnose isomerase
- α-APS, α-d-allopyranose
- α-RPS, α-l-rhamnopyranose
- β-RPS, β-l-rhamnopyranose
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Yoshida H, Yamashita S, Teraoka M, Itoh A, Nakakita SI, Nishi N, Kamitori S. X-ray structure of a protease-resistant mutant form of human galectin-8 with two carbohydrate recognition domains. FEBS J 2012; 279:3937-51. [PMID: 22913484 DOI: 10.1111/j.1742-4658.2012.08753.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 08/14/2012] [Accepted: 08/16/2012] [Indexed: 11/28/2022]
Abstract
Galectin-8 is a tandem-repeat-type β-galactoside-specific animal lectin possessing N-terminal and C-terminal carbohydrate recognition domains (N-CRD and C-CRD, respectively), with a difference in carbohydrate-binding specificity, involved in cell-matrix interaction, malignant transformation, and cell adhesion. N-CRD shows strong affinity for α2-3-sialylated oligosaccharides, a feature unique to galectin-8. C-CRD usually shows lower affinity for oligosaccharides but higher affinity for N-glycan-type branched oligosaccharides than does N-CRD. There have been many structural studies on galectins with a single carbohydrate recognition domain (CRD), but no X-ray structure of a galectin containing both CRDs has been reported. Here, the X-ray structure of a protease-resistant mutant form of human galectin-8 possessing both CRDs and the novel pseudodimer structure of galectin-8 N-CRD in complexes with α2-3-sialylated oligosaccharide ligands were determined. The results revealed a difference in specificity between N-CRD and C-CRD, and provided new insights into the association of CRDs and/or molecules of galectin-8.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, Kagawa, Japan
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Yamashita S, Yoshida H, Uchiyama N, Nakakita Y, Nakakita SI, Tonozuka T, Oguma K, Nishikawa A, Kamitori S. Carbohydrate recognition mechanism of HA70 from Clostridium botulinum deduced from X-ray structures in complexes with sialylated oligosaccharides. FEBS Lett 2012; 586:2404-10. [PMID: 22684008 DOI: 10.1016/j.febslet.2012.05.055] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 05/20/2012] [Accepted: 05/26/2012] [Indexed: 10/28/2022]
Abstract
Clostridium botulinum produces the botulinum neurotoxin, forming a large complex as progenitor toxins in association with non-toxic non-hemagglutinin and/or several different hemagglutinin (HA) subcomponents, HA33, HA17 and HA70, which bind to carbohydrate of glycoproteins from epithelial cells in the infection process. To elucidate the carbohydrate recognition mechanism of HA70, X-ray structures of HA70 from type C toxin (HA70/C) in complexes with sialylated oligosaccharides were determined, and a binding assay by the glycoconjugate microarray was performed. These results suggested that HA70/C can recognize both α2-3- and α2-6-sialylated oligosaccharides, and that it has a higher affinity for α2-3-sialylated oligosaccharides.
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Affiliation(s)
- Satoshi Yamashita
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Kita-gun, Kagawa 761-0793, Japan
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Yoshida H, Teraoka M, Yoshihara A, Izumori K, Kamitori S. Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28. Acta Crystallogr Sect F Struct Biol Cryst Commun 2011; 67:1281-4. [PMID: 22102048 DOI: 10.1107/s1744309111030351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 07/27/2011] [Indexed: 05/26/2023]
Abstract
Acinetobacter sp. L-ribose isomerase (L-RI) catalyzes a reversible isomerization reaction between L-ribose and L-ribulose. To date, information on L-RI remains limited and its amino-acid sequence shows no similarity to those of any known enzymes. Here, recombinant His-tagged L-RI was successfully overexpressed, purified and crystallized. Crystals of His-tagged L-RI were obtained by the hanging-drop vapour-diffusion method at room temperature as two crystal forms which belonged to the monoclinic space group C2, with unit-cell parameters a = 96.60, b = 105.89, c = 71.83 Å, β = 118.16°, and the orthorhombic space group F222, with unit-cell parameters a = 96.44, b = 106.26, c = 117.83 Å. Diffraction data were collected to 3.1 and 2.2 Å resolution, respectively.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Kita-gun, Kagawa 761-0795, Japan
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Kamitori S, Ueda A, Tahara Y, Yoshida H, Ishii T, Uenishi J. Crystal structures of rare disaccharides, α-d-glucopyranosyl β-d-psicofuranoside, and α-d-galactopyranosyl β-d-psicofuranoside. Carbohydr Res 2011; 346:1182-5. [DOI: 10.1016/j.carres.2011.04.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 03/24/2011] [Accepted: 04/03/2011] [Indexed: 11/24/2022]
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Matsumura H, Matsuda K, Nakamura N, Ohtaki A, Yoshida H, Kamitori S, Yohda M, Ohno H. Monooxygenation by a thermophilic cytochrome P450 via direct electron donation from NADH. Metallomics 2011; 3:389-95. [PMID: 21359359 DOI: 10.1039/c0mt00079e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The catalysis of cytochrome P450s requires two-electron donation for the activation of an oxygen molecule. Here, we report the enzymatic catalysis of cytochrome P450, CYP119A2 (P450st), from a thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7, with NAD(P)H as an electron donor and no redox partners and the crystallographic analysis of P450st at high resolution. P450st can catalyse styrene epoxidation with either NADH or NADPH as an electron donor. The P450st reaction with NADH exhibited a sequential mechanism. X-ray crystallography at a resolution of 1.94 Å revealed a sufficiently large heme pocket for NAD(P)H binding and a novel contiguous channel from the active site to bulk solvent in the distal heme pocket. The narrow channel may transfer protons or water to the heme pocket even when a bulky compound, such as NAD(P)H, binds in the pocket. In addition, the F/G loop region (Leu151-Glu156), located around the substrate channel, was deleted in the mutant and constructed to improve the accessibility of NAD(P)H to the heme pocket. Kinetic properties of the Δ151-156 mutant were compared with those of the wild-type P450st. The K(m) value of the mutant was about 2 times lower than that of the wild-type. The results indicated that NAD(P)H could provide the electrons for P450st within the heme pocket.
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Affiliation(s)
- Hirotoshi Matsumura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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Yoshida H, Teraoka M, Nishi N, Nakakita SI, Nakamura T, Hirashima M, Kamitori S. X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose. J Biol Chem 2010; 285:36969-76. [PMID: 20861009 PMCID: PMC2978625 DOI: 10.1074/jbc.m110.163402] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2010] [Revised: 09/02/2010] [Indexed: 01/25/2023] Open
Abstract
Galectin-9, a tandem-repeat-type β-galactoside-specific animal lectin with two carbohydrate recognition domains (CRDs) at the N- and C-terminal ends, is involved in chemoattraction, apoptosis, and the regulation of cell differentiation and has anti-allergic effects. Its ability to recognize carbohydrates is essential for its biological functions. Human galectin-9 (hG9) has high affinity for branched N-glycan-type oligosaccharides (dissociation constants of 0.16-0.70 μM) and linear β1-3-linked poly-N-acetyllactosamines (0.09-8.3 μM) and significant affinity for the α2-3-sialylated oligosaccharides (17-34 μM). Further, its N-terminal CRD (hG9N) and C-terminal CRD (hG9C) differ in specificity. To elucidate this unique feature of hG9, x-ray structures of hG9C in the free form and in complexes with N-acetyllactosamine, the biantennary pyridylaminated oligosaccharide, and α2-3-sialyllactose were determined. They are the first x-ray structural analysis of C-terminal CRD of the tandem-repeat-type galectin. The results clearly revealed the mechanism by which branched and α2-3-sialylated oligosaccharides are recognized and explained the difference in specificity between hG9N and hG9C. Based on structural comparisons with other galectins, we propose that the wide entrance for ligand binding and the shallow binding site of hG9C are favorable for branched oligosaccharides and that Arg(221) is responsible for recognizing sialylated oligosaccharides.
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Affiliation(s)
| | | | | | | | | | - Mitsuomi Hirashima
- Department of Immunology and Immunopathology, Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Yoshida H, Takeda K, Izumori K, Kamitori S. Elucidation of the role of Ser329 and the C-terminal region in the catalytic activity of Pseudomonas stutzeri L-rhamnose isomerase. Protein Eng Des Sel 2010; 23:919-27. [PMID: 20977999 DOI: 10.1093/protein/gzq077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pseudomonas stutzeri l-rhamnose isomerase (l-RhI) is capable of catalyzing the isomerization between various aldoses and ketoses, showing high catalytic activity with broad substrate-specificity compared with Escherichia coli l-RhI. In a previous study, the crystal structure of P. stutzeri l-RhI revealed an active site comparable with that of E. coli l-RhI and d-xylose isomerases (d-XIs) with structurally conserved amino acids, but also with a different residue seemingly responsible for the specificity of P. stutzeri l-RhI, though the residue itself does not interact with the bound substrate. This residue, Ser329, corresponds to Phe336 in E. coli l-RhI and Lys294 in Actinoplanes missouriensis d-XI. To elucidate the role of Ser329 in P. stutzeri l-RhI, we constructed mutants, S329F (E. coli l-RhI type), S329K (A. missouriensis d-XI type), S329L and S329A. Analyses of the catalytic activity and crystal structure of the mutants revealed a hydroxyl group of Ser329 to be crucial for catalytic activity via interaction with a water molecule. In addition, in complexes with substrate, the mutants S329F and S329L exhibited significant electron density in the C-terminal region not observed in the wild-type P. stutzeri l-RhI. The C-terminal region of P. stutzeri l-RhI has flexibility and shows a flip-flop movement at the inter-molecular surface of the dimeric form.
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Affiliation(s)
- Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Takeda K, Yoshida H, Izumori K, Kamitori S. X-ray structures of Bacillus pallidus d-arabinose isomerase and its complex with l-fucitol. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2010; 1804:1359-68. [DOI: 10.1016/j.bbapap.2010.01.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 01/14/2010] [Accepted: 01/25/2010] [Indexed: 11/26/2022]
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Yoshida H, Yamaji M, Ishii T, Izumori K, Kamitori S. Catalytic reaction mechanism of Pseudomonas stutzeri l-rhamnose isomerase deduced from X-ray structures. FEBS J 2010; 277:1045-57. [DOI: 10.1111/j.1742-4658.2009.07548.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yoshida H, Kamitori S. [Catalytic reaction mechanisms of the enzymes producing rare sugars based on X-ray structures]. Seikagaku 2009; 81:811-815. [PMID: 19882953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center & Faculty of Medicine, Kagawa University, Japan
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Kobayashi J, Yoshida H, Chu HN, Yoshikane Y, Kamitori S, Yagi T. Crystallization and preliminary X-ray analysis of AAMS amidohydrolase, the final enzyme in degradation pathway I of pyridoxine. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:829-31. [PMID: 19652351 PMCID: PMC2720345 DOI: 10.1107/s1744309109026864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 07/09/2009] [Indexed: 11/10/2022]
Abstract
alpha-(N-Acetylaminomethylene)succinic acid (AAMS) amidohydrolase from Mesorhizobium loti MAFF303099, which is involved in a degradation pathway of vitamin B(6) and catalyzes the degradation of AAMS to acetic acid, ammonia, carbon dioxide and succinic semialdehyde, has been overexpressed in Escherichia coli. To elucidate the reaction mechanism based on the tertiary structure, the recombinant enzyme was purified and crystallized by the sitting-drop vapour-diffusion method using PEG 8000 as precipitant. A crystal of the enzyme belonged to the monoclinic space group C2, with unit-cell parameters a = 393.2, b = 58.3, c = 98.9 A, beta = 103.4 degrees , and diffraction data were collected to 2.7 A resolution. The V(M) value and calculation of the self-rotation function suggested that three dimers with a threefold symmetry were possibly present in the asymmetric unit.
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Affiliation(s)
- Jun Kobayashi
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Huy Nhat Chu
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Yu Yoshikane
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Toshiharu Yagi
- Faculty of Agriculture and Agricultural Science Program, Graduate School of Integral Arts and Science, Kochi University, Nankoku, Kochi 783-8502, Japan
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Yoshida H, Nishi N, Nakakita SI, Kamitori S. Crystallization and preliminary X-ray diffraction analysis of a protease-resistant mutant form of human galectin-8. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:512-4. [PMID: 19407390 DOI: 10.1107/s1744309109013554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Accepted: 04/10/2009] [Indexed: 11/10/2022]
Abstract
A crystal of a protease-resistant mutant form of human galectin-8, a tandem-repeat-type galectin with two carbohydrate-recognition domains, was obtained using the hanging-drop method and was found to belong to the tetragonal space group P4(3)2(1)2, with unit-cell parameters a = 78.93, b = 78.93, c = 132.05 A. Diffraction data were collected to a resolution of 3.4 A.
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Affiliation(s)
- Hiromi Yoshida
- Life Science Research Center, Kagawa University, Ikenobe, Miki-cho, Kita-gun, Japan
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Matsumoto N, Yamada M, Kurakata Y, Yoshida H, Kamitori S, Nishikawa A, Tonozuka T. Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein. FEBS J 2009; 276:3008-19. [PMID: 19490104 DOI: 10.1111/j.1742-4658.2009.07020.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The crystal structures of Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein (TvuCMBP) complexed with alpha-cyclodextrin (alpha-CD), beta-cyclodextrin (beta-CD) and maltotetraose (G4) have been determined. A common functional conformational change among all solute-binding proteins involves switching from an open form to a closed form, which facilitates transporter binding. Escherichia coli maltodextrin-binding protein (EcoMBP), which is structurally homologous to TvuCMBP, has been determined to adopt the open form when complexed with beta-CD and the closed form when bound to G4. Here, we show that, unlike EcoMBP, TvuCMBP-alpha-CD and TvuCMBP-beta-CD adopt the closed form when complexed, whereas TvuCMBP-G4 adopts the open form. Only two glucose residues are evident in the TvuCMBP-G4 structure, and these bind to the C-domain of TvuCMBP in a manner similar to the way in which maltose binds to the C-domain of EcoMBP. The superposition of TvuCMBP-alpha-CD, TvuCMBP-beta-CD and TvuCMBP-gamma-CD shows that the positions and the orientations of three glucose residues in the cyclodextrin molecules overlay remarkably well. In addition, most of the amino acid residues interacting with these three glucose residues also participate in interactions with the two glucose residues in TvuCMBP-G4, regardless of whether the protein is in the closed or open form. Our results suggest that the mechanisms by which TvuCMBP changes from the open to the closed conformation and maintains the closed form appear to be different from those of EcoMBP, despite the fact that the amino acid residues responsible for the initial binding of the ligands are well conserved between TvuCMBP and EcoMBP.
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Affiliation(s)
- Naoki Matsumoto
- Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Japan
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Watanabe Y, Yoshida H, Takeda K, Ishi T, Kamitori S. β-d-Altrose. Acta Crystallogr Sect E Struct Rep Online 2009; 65:o280. [PMID: 21581893 PMCID: PMC2968302 DOI: 10.1107/s1600536809000397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2008] [Accepted: 01/06/2009] [Indexed: 05/30/2023]
Abstract
The mol-ecule of the title compound, C(6)H(12)O(6), [systematic name: (2R,3S,4R,5R,6R)-6-(hydroxy-meth-yl)oxane-2,3,4,5-tetrol] adopts a (4)C(1) chair conformation with the anomeric hydroxyl group in the equatorial position. All hydroxyl groups act as donors and acceptors in hydrogen bonding and the mol-ecule is involved in ten inter-molecular O-H⋯O inter-actions [O⋯O = 2.672 (5)-2.776 (4) Å] with eight neighbouring mol-ecules. Two independent O-H⋯O-H⋯ helices extending along the z axis are found in this structure.
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Affiliation(s)
- Yuji Watanabe
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Kosei Takeda
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Tomohiko Ishi
- Faculty of Engineering, Kagawa University, 2217-20 Hayashi-machi, Takamatsu, Kagawa 761-0396, Japan
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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Kurakata Y, Uechi A, Yoshida H, Kamitori S, Sakano Y, Nishikawa A, Tonozuka T. Corrigendum to “Structural Insights into the Substrate Specificity and Function of Escherichia coli K12 YgjK, a Glucosidase Belonging to the Glycoside Hydrolase Family 63” [J. Mol. Biol. 381 (2008) 116–128]. J Mol Biol 2008. [DOI: 10.1016/j.jmb.2008.08.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Takeda K, Yoshida H, Takada G, Izumori K, Kamitori S. Overexpression, purification, crystallization and preliminary X-ray crystal analysis of Bacillus pallidusD-arabinose isomerase. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:945-8. [PMID: 18931442 PMCID: PMC2564884 DOI: 10.1107/s1744309108028352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 09/04/2008] [Indexed: 11/10/2022]
Abstract
D-Arabinose isomerase catalyzes the isomerization of D-arabinose to D-ribulose. Bacillus pallidus D-arabinose isomerase has broad substrate specificity and can catalyze the isomerization of D-arabinose, L-fucose, L-xylose, L-galactose and D-altrose. Recombinant B. pallidus D-arabinose isomerase was overexpressed, purified and crystallized. A crystal of the enzyme was obtained by the sitting-drop method at room temperature and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 144.9, b = 127.9, c = 109.5 A. Diffraction data were collected to 2.3 A resolution.
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Affiliation(s)
- Kosei Takeda
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Hiromi Yoshida
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
| | - Goro Takada
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Ken Izumori
- Department of Biochemistry and Food Science, Faculty of Agriculture and Rare Sugar Research Center, Kagawa University, Miki-cho, Kagawa 761-0795, Japan
| | - Shigehiro Kamitori
- Division of Structural Biology, Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
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