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Ohno S, Manabe N, Yamaguchi T, Uzawa J, Yamaguchi Y. Ribitol in Solution Is an Equilibrium of Asymmetric Conformations. Molecules 2021; 26:molecules26185471. [PMID: 34576942 PMCID: PMC8468352 DOI: 10.3390/molecules26185471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/06/2021] [Indexed: 11/18/2022] Open
Abstract
Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3–C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2–C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR has identical chemical shifts for C1 and C5. NMR 3J coupling constants and OH exchange rates suggest that ribitol is an equilibrium of conformations, under the influence of hydrogen bonds and/or steric hinderance. Molecular dynamics (MD) simulations allowed us to discuss such a chemically symmetric molecule, pinpointing the presence of asymmetric conformations evidenced by the presence of correlations between C2–C3 and C3–C4 dihedral angles. These findings provide a basis for understanding the dynamic structure of ribitol and the function of ribitol-binding enzymes.
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Affiliation(s)
- Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan; (S.O.); (N.M.)
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan; (S.O.); (N.M.)
| | - Takumi Yamaguchi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi 923-1292, Ishikawa, Japan;
| | - Jun Uzawa
- Structural Glycobiology Team, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Saitama, Japan;
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan; (S.O.); (N.M.)
- Structural Glycobiology Team, RIKEN (The Institute of Physical and Chemical Research), 2-1 Hirosawa, Wako 351-0198, Saitama, Japan;
- Correspondence: ; Tel.: +81-22-727-0208
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Singh A, Rai SK, Manisha M, Yadav SK. Immobilized L-ribose isomerase for the sustained synthesis of a rare sugar D-talose. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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A review on l-ribose isomerases for the biocatalytic production of l-ribose and l-ribulose. Food Res Int 2021; 145:110409. [PMID: 34112412 DOI: 10.1016/j.foodres.2021.110409] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/08/2021] [Accepted: 05/06/2021] [Indexed: 11/21/2022]
Abstract
Presently, because of the extraordinary roles and potential applications, rare sugars turn into a focus point for countless researchers in the field of carbohydrates. l-ribose and l-ribulose are rare sugars and isomers of each other. This aldo and ketopentose are expensive but can be utilized as an antecedent for the manufacturing of various rare sugars and l-nucleoside analogue. The bioconversion approach turns into an excellent alternative method to l-ribulose and l-ribose production, as compared to the complex and lengthy chemical methods. The basic purpose of this research was to describe the importance of rare sugars in various fields and their easy production by using enzymatic methods. l-Ribose isomerase (L-RI) is an enzyme discovered by Tsuyoshi Shimonishi and Ken Izumori in 1996 from Acinetobacter sp. strain DL-28. L-RI structure was cupin-type-β-barrel shaped with a catalytic site between two β-sheets surrounded by metal ions. The crystal structures of the L-RI showed that it contains a homotetramer structure. Current review have concentrated on the sources, characteristics, applications, conclusions and future prospects including the potentials of l-ribose isomerase for the commercial production of l-ribose and l-ribulose. The MmL-RIse and CrL-RIse have the potential to produce the l-ribulose up to 32% and 31%, respectively. The CrL-RIse is highly stable as compared to other L-RIs. The results explained that the L-RIs have great potential in the production of rare sugars especially, l-ribose and l-ribulose, while the immobilization technique can enhance its functionality and properties. The present study precises the applications of L-RIs acquired from various sources for l-ribose and l-ribulose production.
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Mahmood S, Iqbal MW, Riaz T, Zhang W, Mu W. Characterization of recombinant L-ribose isomerase acquired from Cryobacterium sp. N21 with potential application in L-ribulose production. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.06.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Mahmood S, Iqbal MW, Riaz T, Hassanin HA, Zhu Y, Ni D, Mu W. Characterization of a recombinant l-ribose isomerase from Mycetocola miduiensis and its application for the production of l-ribulose. Enzyme Microb Technol 2020; 135:109510. [DOI: 10.1016/j.enzmictec.2020.109510] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/08/2020] [Accepted: 01/12/2020] [Indexed: 11/30/2022]
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Toxvaerd S. The start of the Abiogenesis: Preservation of homochirality in proteins as a necessary and sufficient condition for the establishment of the metabolism. J Theor Biol 2018; 451:117-121. [DOI: 10.1016/j.jtbi.2018.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/02/2018] [Accepted: 05/03/2018] [Indexed: 11/24/2022]
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Tseng WC, Wu TJ, Chang YJ, Cheng HW, Fang TY. Overexpression and characterization of a recombinant l -ribose isomerase from Actinotalea fermentans ATCC 43279. J Biotechnol 2017; 259:168-174. [DOI: 10.1016/j.jbiotec.2017.07.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 06/19/2017] [Accepted: 07/21/2017] [Indexed: 11/25/2022]
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l-Ribose isomerase and mannose-6-phosphate isomerase: properties and applications for l-ribose production. Appl Microbiol Biotechnol 2016; 100:9003-9011. [DOI: 10.1007/s00253-016-7834-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 11/27/2022]
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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] [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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Widderich N, Kobus S, Höppner A, Riclea R, Seubert A, Dickschat JS, Heider J, Smits SHJ, Bremer E. Biochemistry and Crystal Structure of Ectoine Synthase: A Metal-Containing Member of the Cupin Superfamily. PLoS One 2016; 11:e0151285. [PMID: 26986827 PMCID: PMC4795551 DOI: 10.1371/journal.pone.0151285] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/25/2016] [Indexed: 01/24/2023] Open
Abstract
Ectoine is a compatible solute and chemical chaperone widely used by members of the Bacteria and a few Archaea to fend-off the detrimental effects of high external osmolarity on cellular physiology and growth. Ectoine synthase (EctC) catalyzes the last step in ectoine production and mediates the ring closure of the substrate N-gamma-acetyl-L-2,4-diaminobutyric acid through a water elimination reaction. However, the crystal structure of ectoine synthase is not known and a clear understanding of how its fold contributes to enzyme activity is thus lacking. Using the ectoine synthase from the cold-adapted marine bacterium Sphingopyxis alaskensis (Sa), we report here both a detailed biochemical characterization of the EctC enzyme and the high-resolution crystal structure of its apo-form. Structural analysis classified the (Sa)EctC protein as a member of the cupin superfamily. EctC forms a dimer with a head-to-tail arrangement, both in solution and in the crystal structure. The interface of the dimer assembly is shaped through backbone-contacts and weak hydrophobic interactions mediated by two beta-sheets within each monomer. We show for the first time that ectoine synthase harbors a catalytically important metal co-factor; metal depletion and reconstitution experiments suggest that EctC is probably an iron-dependent enzyme. We found that EctC not only effectively converts its natural substrate N-gamma-acetyl-L-2,4-diaminobutyric acid into ectoine through a cyclocondensation reaction, but that it can also use the isomer N-alpha-acetyl-L-2,4-diaminobutyric acid as its substrate, albeit with substantially reduced catalytic efficiency. Structure-guided site-directed mutagenesis experiments targeting amino acid residues that are evolutionarily highly conserved among the extended EctC protein family, including those forming the presumptive iron-binding site, were conducted to functionally analyze the properties of the resulting EctC variants. An assessment of enzyme activity and iron content of these mutants give important clues for understanding the architecture of the active site positioned within the core of the EctC cupin barrel.
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Affiliation(s)
- Nils Widderich
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Stefanie Kobus
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Astrid Höppner
- X-ray Facility and Crystal Farm, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ramona Riclea
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Andreas Seubert
- Department of Chemistry, Analytical Chemistry, Philipps-Universität Marburg, Marburg, Germany
| | - Jeroen S. Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
- Institute of Organic Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Johann Heider
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
| | - Sander H. J. Smits
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- * E-mail: (SS); (EB)
| | - Erhard Bremer
- Department of Biology, Laboratory for Microbiology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Philipps-University Marburg, D-35043 Marburg, Germany
- * E-mail: (SS); (EB)
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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] [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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