Publications
28 results found
Ghilarov D, Inaba-Inoue S, Stepien P, et al., 2021, Molecular mechanism of SbmA, a promiscuous transporter exploited by antimicrobial peptides, Science Advances, Vol: 7, Pages: 1-10, ISSN: 2375-2548
Antibiotic metabolites and antimicrobial peptides mediate competition between bacterial species. Many of them hijack inner and outer membrane proteins to enter cells. Sensitivity of enteric bacteria to multiple peptide antibiotics is controlled by the single inner membrane protein SbmA. To establish the molecular mechanism of peptide transport by SbmA and related BacA, we determined their cryo–electron microscopy structures at 3.2 and 6 Å local resolution, respectively. The structures show a previously unknown fold, defining a new class of secondary transporters named SbmA-like peptide transporters. The core domain includes conserved glutamates, which provide a pathway for proton translocation, powering transport. The structures show an outward-open conformation with a large cavity that can accommodate diverse substrates. We propose a molecular mechanism for antibacterial peptide uptake paving the way for creation of narrow-targeted therapeutics.
Inaba S, Shiota A, Yoshida T, et al., 2019, Site-specific observation of the conformational change of a protein with N-15-labeled Tyr residues using NMR, ANALYTICAL BIOCHEMISTRY, Vol: 574, Pages: 34-38, ISSN: 0003-2697
Oda M, Xi Z, Inaba S, et al., 2019, Binding thermodynamics of metal ions to HIV-1 ribonuclease H domain, JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, Vol: 135, Pages: 2647-2653, ISSN: 1388-6150
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- Citations: 6
Inaba S, Kamiya N, Bekker G-J, et al., 2019, Folding thermodynamics of PET-hydrolyzing enzyme Cut190 depending on Ca2+ concentration, JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, Vol: 135, Pages: 2655-2663, ISSN: 1388-6150
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- Citations: 21
Hosoe Y, Numoto N, Inaba S, et al., 2019, Structural and functional properties of Grb2 SH2 dimer in CD28 binding, BIOPHYSICS AND PHYSICOBIOLOGY, Vol: 16, Pages: 80-88
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- Citations: 8
Inaba-Inoue S, Inoue K, Hikima T, et al., 2019, CRYSTAL AND SOLUTION STRUCTURES OF SH2 DOMAIN OF SIGNALING MOLECULE IN COMPLEX WITH THE CO-STIMULATORY RECEPTOR CD28, ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES, Vol: 75, Pages: E69-E69, ISSN: 2053-2733
Oda M, Yamagami Y, Inaba S, et al., 2018, Enzymatic hydrolysis of PET: functional roles of three Ca2+ ions bound to a cutinase-like enzyme, Cut190*, and its engineering for improved activity, APPLIED MICROBIOLOGY AND BIOTECHNOLOGY, Vol: 102, Pages: 10067-10077, ISSN: 0175-7598
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- Citations: 51
Numoto N, Kamiya N, Bekker G-J, et al., 2018, Structural Dynamics of the PET-Degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-Bound States Elucidates the Ca2+-Driven Catalytic Cycle, BIOCHEMISTRY, Vol: 57, Pages: 5289-5300, ISSN: 0006-2960
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- Citations: 36
Hosoe Y, Inaba S, Sekiguchi H, et al., 2018, DNA-binding induced conformational change of c-Myb R2R3 analyzed using diffracted X-ray tracking, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, Vol: 503, Pages: 338-343, ISSN: 0006-291X
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- Citations: 3
Oda M, Inaba S, Kamiya N, et al., 2018, Structural and thermodynamic characterization of endo-1,3-beta-glucanase: Insights into the substrate recognition mechanism, BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, Vol: 1866, Pages: 415-425, ISSN: 1570-9639
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- Citations: 14
Shiota A, Inaba S, Oda M, 2018, Effects of active site residues of 3-hydroxysteroid dehydrogenase from pseudomonas sp b-0831 on its catalysis and cofactor binding, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, Vol: 82, Pages: 1702-1707, ISSN: 0916-8451
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- Citations: 2
Inaba S, Fukada H, Oda M, 2018, Effect of a salt-bridge between inter-repeats on the 3D structure of the c-Myb DNA-binding domain revealed by thermodynamic analysis, JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, Vol: 131, Pages: 335-341, ISSN: 1388-6150
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- Citations: 8
Usui D, Inaba S, Kamatari YO, et al., 2017, Light-chain residue 95 is critical for antigen binding and multispecificity of monoclonal antibody G2, BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, Vol: 490, Pages: 1205-1209, ISSN: 0006-291X
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- Citations: 4
Usui D, Inaba S, Sekiguchi H, et al., 2017, First observation of metal ion-induced structural fluctuations of alpha-helical peptides by using diffracted X-ray tracking, BIOPHYSICAL CHEMISTRY, Vol: 228, Pages: 81-86, ISSN: 0301-4622
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- Citations: 4
Miki A, Inaba S, Maruno T, et al., 2017, Tryptophan introduction can change -glucan binding ability of the carbohydrate-binding module of endo-1,3--glucanase, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, Vol: 81, Pages: 951-957, ISSN: 0916-8451
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- Citations: 2
Sato Y, Inaba S, Fukada H, et al., 2017, Pronounced effect of hapten binding on thermal stability of an anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain, MOLECULAR IMMUNOLOGY, Vol: 85, Pages: 130-136, ISSN: 0161-5890
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- Citations: 2
Inaba S, Numoto N, Ogawa S, et al., 2017, Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 292, Pages: 1052-1060
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- Citations: 15
INABA S, 2017, Structural and Functional Analysis of DNA-binding Protein under Physiological Conditions, Seibutsu Butsuri, Vol: 57, Pages: 257-258, ISSN: 0582-4052
Sato Y, Tanaka Y, Inaba S, et al., 2016, Structural dynamics of a single-chain Fv antibody against (4-hydroxy-3-nitrophenyl)acetyl, INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, Vol: 91, Pages: 151-157, ISSN: 0141-8130
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- Citations: 12
Oda M, Tanabe Y, Noda M, et al., 2016, Structural and binding properties of laminarin revealed by analytical ultracentrifugation and calorimetric analyses, CARBOHYDRATE RESEARCH, Vol: 431, Pages: 33-38, ISSN: 0008-6215
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- Citations: 9
Inaba S, Fukada H, Oda M, 2016, Thermodynamic effects of a linker region between two repeats of a protein, c-Myb R2R3, on its stability and structural dynamics, JOURNAL OF THERMAL ANALYSIS AND CALORIMETRY, Vol: 123, Pages: 1763-1767, ISSN: 1388-6150
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- Citations: 4
Inaba S, Fukada H, Oda M, 2016, Folding thermodynamics of c-Myb DNA-binding domain in correlation with its alpha-helical contents, INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES, Vol: 82, Pages: 725-732, ISSN: 0141-8130
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- Citations: 6
Inaba S, Maeno A, Sakurai K, et al., 2015, Functional conformer of c-Myb DNA-binding domain revealed by variable temperature studies, FEBS JOURNAL, Vol: 282, Pages: 4497-4514, ISSN: 1742-464X
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- Citations: 7
Miki A, Inaba S, Baba T, et al., 2015, Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, Vol: 79, Pages: 1603-1607, ISSN: 0916-8451
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- Citations: 11
Inaba S, Fukada H, Ikegami T, et al., 2013, Thermodynamic effects of multiple protein conformations on stability and DNA binding, ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, Vol: 537, Pages: 225-232, ISSN: 0003-9861
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- Citations: 26
Nakabayashi M, Tsukahara Y, Iwasaki-Miyamoto Y, et al., 2013, Crystal Structures of Hereditary Vitamin D-Resistant Rickets-Associated Vitamin D Receptor Mutants R270L and W282R Bound to 1,25-Dihydroxyvitamin D-3 and Synthetic Ligands, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 56, Pages: 6745-6760, ISSN: 0022-2623
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- Citations: 20
Travin DY, Vigouroux A, Inaba-Inoue S, et al., The antibiotic phazolicin displays a dual mode of uptake in Gram-negative bacteria
<jats:title>ABSTRACT</jats:title><jats:p>Phazolicin (PHZ) is a peptide antibiotic exhibiting narrow-spectrum activity against rhizobia closely related to its producer <jats:italic>Rhizobium</jats:italic> sp. Pop5. Using genetic and biochemical techniques, we here identified BacA and YejABEF as two importers of PHZ in a sensitive model strain <jats:italic>Sinorhizobium meliloti</jats:italic> Sm1021. BacA and YejABEF are members of SLiPT and ABC transporter families of non-specific peptide importers, respectively. The uptake of PHZ by two distinct families of transporters dramatically decreases the naturally occurring rate of resistance. Moreover, since both BacA and YejABEF are essential for the development of functional symbiosis of rhizobia with leguminous plants, the acquisition of PHZ resistance via the inactivation of transporters is further disfavoured since single <jats:italic>bacA</jats:italic> or <jats:italic>yejABEF</jats:italic> mutants are unable to propagate in root nodules. Crystal structures of the periplasmic subunit YejA from <jats:italic>S. meliloti</jats:italic> and <jats:italic>Escherichia coli</jats:italic> revealed fortuitous bound peptides, suggesting a non-specific peptide-binding mechanism that facilitates the uptake of PHZ and other antimicrobial peptides.</jats:p><jats:sec><jats:title>SIGNIFICANCE</jats:title><jats:p>Many bacteria produce antimicrobial peptides to eliminate competitors and create an exclusive niche. These peptides kill bacteria by either membrane disruption or inhibiting essential intracellular processes. The Achilles heel of the latter type of antimicrobials is their dependence on transporters to enter the susceptible bacteria since mutations in such transporters result in resistance. We describe here how the ribosome-targeting peptide phazolicin, produced by <jats:italic>Rhizobium</jats:italic&g
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