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  1. Article ; Online: Reversible Photoreaction of a Retinal Photoisomerase, Retinal G-Protein-Coupled Receptor RGR.

    Morimoto, Naoya / Nagata, Takashi / Inoue, Keiichi

    Biochemistry

    2023  Volume 62, Issue 9, Page(s) 1429–1432

    Abstract: Retinal G-protein-coupled receptor (RGR) plays a crucial role in the visual system of vertebrates as a retinal photoisomerase, which isomerizes all- ...

    Abstract Retinal G-protein-coupled receptor (RGR) plays a crucial role in the visual system of vertebrates as a retinal photoisomerase, which isomerizes all-
    MeSH term(s) Animals ; Cattle ; Humans ; Retinaldehyde/chemistry ; Retina ; Receptors, G-Protein-Coupled ; cis-trans-Isomerases ; Eye Proteins/chemistry ; Rhodopsin
    Chemical Substances Retinaldehyde (RR725D715M) ; retinal isomerase ; Receptors, G-Protein-Coupled ; cis-trans-Isomerases (EC 5.2.-) ; Eye Proteins ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2023-04-14
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00084
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  2. Article: Expanding horizons of biosciences by light-control.

    Kataoka, Mikio / Nagata, Takashi

    Biophysics and physicobiology

    2021  Volume 18, Page(s) 13–15

    Language English
    Publishing date 2021-02-02
    Publishing country Japan
    Document type Journal Article
    ISSN 2189-4779
    ISSN 2189-4779
    DOI 10.2142/biophysico.bppb-v18.002
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  3. Article ; Online: Rhodopsins at a glance.

    Nagata, Takashi / Inoue, Keiichi

    Journal of cell science

    2021  Volume 134, Issue 22

    Abstract: Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, ... ...

    Abstract Rhodopsins are photoreceptive membrane proteins consisting of a common heptahelical transmembrane architecture that contains a retinal chromophore. Rhodopsin was first discovered in the animal retina in 1876, but a different type of rhodopsin, bacteriorhodopsin, was reported to be present in the cell membrane of an extreme halophilic archaeon, Halobacterium salinarum, 95 years later. Although these findings were made by physiological observation of pigmented tissue and cell bodies, recent progress in genomic and metagenomic analyses has revealed that there are more than 10,000 microbial rhodopsins and 9000 animal rhodopsins with large diversity and tremendous new functionality. In this Cell Science at a Glance article and accompanying poster, we provide an overview of the diversity of functions, structures, color discrimination mechanisms and optogenetic applications of these two rhodopsin families, and will also highlight the third distinctive rhodopsin family, heliorhodopsin.
    MeSH term(s) Genomics ; Rhodopsin/genetics ; Rhodopsins, Microbial/genetics
    Chemical Substances Rhodopsins, Microbial ; heliorhodopsin ; Rhodopsin (9009-81-8)
    Language English
    Publishing date 2021-11-25
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.258989
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  4. Article: The Significance of

    Nagata, Takashi

    Japan Medical Association journal : JMAJ

    2016  Volume 59, Issue 1, Page(s) 19–24

    Language English
    Publishing date 2016-07-01
    Publishing country Japan
    Document type Review ; Journal Article
    ZDB-ID 2052217-4
    ISSN 1346-8650
    ISSN 1346-8650
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  5. Article ; Online: Enhancing Bioethanol Production from Rice Straw through Environmentally Friendly Delignification Using Versatile Peroxidase.

    Teo, Kenneth Sze Kai / Kondo, Keiko / Khattab, Sadat Mohamed Rezk / Watanabe, Takashi / Nagata, Takashi / Katahira, Masato

    Journal of agricultural and food chemistry

    2024  Volume 72, Issue 5, Page(s) 2657–2666

    Abstract: Rice straw (RS), an agricultural residue rich in carbohydrates, has substantial potential for bioethanol production. However, the presence of lignin impedes access to these carbohydrates, hindering efficient carbohydrate-to-bioethanol conversion. Here, ... ...

    Abstract Rice straw (RS), an agricultural residue rich in carbohydrates, has substantial potential for bioethanol production. However, the presence of lignin impedes access to these carbohydrates, hindering efficient carbohydrate-to-bioethanol conversion. Here, we expressed versatile peroxidase (VP), a lignin-degrading enzyme, in
    MeSH term(s) Lignin/chemistry ; Oryza/chemistry ; Peroxidase/metabolism ; Carbohydrates/chemistry ; Peroxidases/metabolism ; Fermentation ; Hydrolysis
    Chemical Substances Lignin (9005-53-2) ; Peroxidase (EC 1.11.1.7) ; Carbohydrates ; Peroxidases (EC 1.11.1.-)
    Language English
    Publishing date 2024-01-30
    Publishing country United States
    Document type Journal Article
    ZDB-ID 241619-0
    ISSN 1520-5118 ; 0021-8561
    ISSN (online) 1520-5118
    ISSN 0021-8561
    DOI 10.1021/acs.jafc.3c07998
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  6. Article ; Online: Structural Insights into the Interaction between the C-Terminal-Deleted BH3-like Motif Peptide of Hepatitis B Virus X Protein and Bcl-x

    Kusunoki, Hideki / Sakamoto, Taiichi / Kobayashi, Naohiro / Kohno, Toshiyuki / Wakamatsu, Kaori / Nagata, Takashi

    Biochemistry

    2024  Volume 63, Issue 5, Page(s) 632–643

    Abstract: Hepatitis B virus X protein (HBx) plays a crucial role in the development of hepatocellular carcinoma (HCC) associated with hepatitis B virus (HBV) infection. The full-length HBx protein interacts with Bcl- ... ...

    Abstract Hepatitis B virus X protein (HBx) plays a crucial role in the development of hepatocellular carcinoma (HCC) associated with hepatitis B virus (HBV) infection. The full-length HBx protein interacts with Bcl-x
    MeSH term(s) Humans ; Carcinoma, Hepatocellular/metabolism ; Liver Neoplasms/metabolism ; Trans-Activators/chemistry ; Viral Regulatory and Accessory Proteins/metabolism ; bcl-X Protein/chemistry ; Hepatitis B virus/genetics ; Hepatitis B virus/metabolism ; Hepatitis B/complications ; Hepatitis B/pathology
    Chemical Substances hepatitis B virus X protein ; Trans-Activators ; Viral Regulatory and Accessory Proteins ; bcl-X Protein
    Language English
    Publishing date 2024-02-20
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021/acs.biochem.3c00709
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  7. Article ; Online: Complex Formation of an RNA Aptamer with a Part of HIV-1 Tat through Induction of Base Triples in Living Human Cells Proven by In-Cell NMR.

    Eladl, Omar / Yamaoki, Yudai / Kondo, Keiko / Nagata, Takashi / Katahira, Masato

    International journal of molecular sciences

    2023  Volume 24, Issue 10

    Abstract: An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside ... ...

    Abstract An RNA aptamer that strongly binds to a target molecule has the potential to be a nucleic acid drug inside living human cells. To investigate and improve this potential, it is critical to elucidate the structure and interaction of RNA aptamers inside living cells. We examined an RNA aptamer for HIV-1 Tat (TA), which had been found to trap Tat and repress its function in living human cells. We first used in vitro NMR to examine the interaction between TA and a part of Tat containing the binding site for trans-activation response element (TAR). It was revealed that two U-A∗U base triples are formed in TA upon binding of Tat. This was assumed to be critical for strong binding. Then, TA in complex with a part of Tat was incorporated into living human cells. The presence of two U-A∗U base triples was also revealed for the complex in living human cells by in-cell NMR. Thus, the activity of TA in living human cells was rationally elucidated by in-cell NMR.
    MeSH term(s) Humans ; tat Gene Products, Human Immunodeficiency Virus/metabolism ; Aptamers, Nucleotide/chemistry ; HIV-1/metabolism ; Nucleic Acid Conformation ; Magnetic Resonance Spectroscopy ; RNA, Viral/genetics
    Chemical Substances tat Gene Products, Human Immunodeficiency Virus ; Aptamers, Nucleotide ; RNA, Viral
    Language English
    Publishing date 2023-05-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2019364-6
    ISSN 1422-0067 ; 1422-0067 ; 1661-6596
    ISSN (online) 1422-0067
    ISSN 1422-0067 ; 1661-6596
    DOI 10.3390/ijms24109069
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  8. Article ; Online: Structural insights into the molecular mechanisms of substrate recognition and hydrolysis by feruloyl esterase from Aspergillus sydowii.

    Phienluphon, Apisan / Kondo, Keiko / Mikami, Bunzo / Nagata, Takashi / Katahira, Masato

    International journal of biological macromolecules

    2023  Volume 253, Issue Pt 5, Page(s) 127188

    Abstract: The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, ... ...

    Abstract The depolymerization of lignocellulosic biomass is facilitated by feruloyl esterases (FAEs), which hydrolyze ester bonds between lignin and polysaccharides. Fungal FAEs belonging to subfamily (SF) 6 release precursors such as ferulic acid derivatives, attractive for biochemical production. Among these, Aspergillus sydowii FAE (AsFaeE), an SF6 FAE, exhibits remarkable activity across various substrates. In this study, we conducted X-ray crystallography and kinetic analysis to unravel the molecular mechanisms governing substrate recognition and catalysis by AsFaeE. AsFaeE exhibits a typical α/β-hydrolase fold, characterized by a catalytic triad of serine, aspartate, and histidine. Comparative analysis of substrate-free, ferulic acid-bound, and sinapic acid-bound forms of AsFaeE suggests a conformational change in the loop covering the substrate-binding pocket upon binding. Notably, Pro158 and Phe159 within this loop cover the phenolic part of the substrate, forming three layers of planar rings. Our structure-based functional mutagenesis clarifies the roles of the residues involved in substrate binding and catalytic activity. Furthermore, distinct substrate-binding mechanisms between AsFaeE and other studied FAEs are identified. This investigation offers the initial structural insights into substrate recognition by SF6 FAEs, equipping us with structural knowledge that might facilitate the design of FAE variants capable of efficiently processing a wider range of substrate sizes.
    MeSH term(s) Hydrolysis ; Kinetics ; Carboxylic Ester Hydrolases/chemistry ; Substrate Specificity
    Chemical Substances feruloyl esterase (EC 3.1.1.73) ; ferulic acid (AVM951ZWST) ; Carboxylic Ester Hydrolases (EC 3.1.1.-)
    Language English
    Publishing date 2023-09-30
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 282732-3
    ISSN 1879-0003 ; 0141-8130
    ISSN (online) 1879-0003
    ISSN 0141-8130
    DOI 10.1016/j.ijbiomac.2023.127188
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  9. Article ; Online: Chemical shift assignments of a fusion protein comprising the C-terminal-deleted hepatitis B virus X protein BH3-like motif peptide and Bcl-x

    Kusunoki, Hideki / Hamaguchi, Isao / Kobayashi, Naohiro / Nagata, Takashi

    Biomolecular NMR assignments

    2022  Volume 16, Issue 2, Page(s) 357–361

    Abstract: Chronic hepatitis B virus (HBV) infection is a major risk factor for the development of liver diseases including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV has the multifunctional protein, HBV X protein (HBx, 154 residues), which plays ... ...

    Abstract Chronic hepatitis B virus (HBV) infection is a major risk factor for the development of liver diseases including fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). HBV has the multifunctional protein, HBV X protein (HBx, 154 residues), which plays key roles in HBV replication and liver disease development. Interaction of HBx through its BH3-like motif with the anti-apoptotic protein Bcl-x
    MeSH term(s) Apoptosis Regulatory Proteins ; Carcinoma, Hepatocellular/metabolism ; Carcinoma, Hepatocellular/pathology ; Dipeptides/metabolism ; Glycine/metabolism ; Hepatitis B virus/metabolism ; Hepatitis B, Chronic ; Humans ; Liver Neoplasms/metabolism ; Liver Neoplasms/pathology ; Nuclear Magnetic Resonance, Biomolecular ; Serine/metabolism ; Trans-Activators ; Viral Regulatory and Accessory Proteins ; bcl-X Protein/chemistry ; bcl-X Protein/metabolism
    Chemical Substances Apoptosis Regulatory Proteins ; Dipeptides ; Trans-Activators ; Viral Regulatory and Accessory Proteins ; bcl-X Protein ; hepatitis B virus X protein ; Serine (452VLY9402) ; Glycine (TE7660XO1C)
    Language English
    Publishing date 2022-08-31
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2388861-1
    ISSN 1874-270X ; 1874-2718
    ISSN (online) 1874-270X
    ISSN 1874-2718
    DOI 10.1007/s12104-022-10104-4
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  10. Article: Disaster Medicine From International Health Perspective: - The Takemi Program as the origin of the Japan Medical Association Team-.

    Nagata, Takashi

    Japan Medical Association journal : JMAJ

    2014  Volume 57, Issue 1, Page(s) 15–18

    Language English
    Publishing date 2014-08-07
    Publishing country Japan
    Document type Journal Article
    ZDB-ID 2052217-4
    ISSN 1346-8650
    ISSN 1346-8650
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