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  1. Article: Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein

    Watanabe, Seiya / Yoshiwara, Kentaroh / Matsubara, Ryo / Watanabe, Yasunori

    Biochemical and biophysical research communications. 2022 May 14, v. 604

    2022  

    Abstract: l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)⁺-dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway, and is classified into glucose-fructose oxidoreductase and short-chain dehydrogenase/ ... ...

    Abstract l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)⁺-dependent oxidation of l-arabinose to L-arabinono-1,4-lactone in the non-phosphorylative l-arabinose pathway, and is classified into glucose-fructose oxidoreductase and short-chain dehydrogenase/reductase (SDR). We herein report the crystal structure of a SDR-type AraDH (from Herbaspirillum huttiense) for the first time. The interactions between Asp49 and the 2′- and 3′-hydroxyl groups of NAD⁺ were consistent with strict specificity for NAD⁺. In a binding model for the substrate, Ser155 and Tyr168, highly conserved in the SDR superfamily, interacted with the C1 and/or C2 hydroxyl(s) of l-arabinose, whereas interactions between Asp107, Arg109, and Gln206 and the C2 and/or C3 hydroxyl(s) were unique to AraDH. Trp200 significantly contributed to the selectivities of the C4 hydroxyl and C6 methyl of substrates.
    Keywords Herbaspirillum ; arabinose ; crystal structure ; models ; oxidation ; oxidoreductases ; research
    Language English
    Dates of publication 2022-0514
    Size p. 14-21.
    Publishing place Elsevier Inc.
    Document type Article
    ZDB-ID 205723-2
    ISSN 0006-291X ; 0006-291X
    ISSN (online) 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2022.03.028
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

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  2. Article ; Online: Crystal structure of L-arabinose 1-dehydrogenase as a short-chain reductase/dehydrogenase protein.

    Watanabe, Seiya / Yoshiwara, Kentaroh / Matsubara, Ryo / Watanabe, Yasunori

    Biochemical and biophysical research communications

    2022  Volume 604, Page(s) 14–21

    Abstract: l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P) ...

    Abstract l-Arabinose 1-dehydrogenase (AraDH) catalyzes the NAD(P)
    MeSH term(s) Arabinose/chemistry ; NAD/metabolism ; Oxidoreductases/metabolism ; Short Chain Dehydrogenase-Reductases/metabolism ; Substrate Specificity
    Chemical Substances NAD (0U46U6E8UK) ; Arabinose (B40ROO395Z) ; Oxidoreductases (EC 1.-) ; Short Chain Dehydrogenase-Reductases (EC 1.1.1.-)
    Language English
    Publishing date 2022-03-08
    Publishing country United States
    Document type Journal Article
    ZDB-ID 205723-2
    ISSN 1090-2104 ; 0006-291X ; 0006-291X
    ISSN (online) 1090-2104 ; 0006-291X
    ISSN 0006-291X
    DOI 10.1016/j.bbrc.2022.03.028
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 116: Show issues Location:
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    ab Jg. 2022: Lesesaal (EG)

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  3. Article ; Online: Incommensurate grain-boundary atomic structure.

    Seki, Takehito / Futazuka, Toshihiro / Morishige, Nobusato / Matsubara, Ryo / Ikuhara, Yuichi / Shibata, Naoya

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7806

    Abstract: Grain-boundary atomic structures of crystalline materials have long been believed to be commensurate with the crystal periodicity of the adjacent crystals. In the present study, we experimentally observed a Σ9 grain-boundary atomic structure of a bcc ... ...

    Abstract Grain-boundary atomic structures of crystalline materials have long been believed to be commensurate with the crystal periodicity of the adjacent crystals. In the present study, we experimentally observed a Σ9 grain-boundary atomic structure of a bcc crystal (Fe-3%Si). It is found that the Σ9 grain-boundary structure is largely reconstructed and forms a dense packing of icosahedral clusters in its core. Combining with the detailed theoretical calculations, the Σ9 grain-boundary atomic structure is discovered to be incommensurate with the adjacent crystal structures. The present findings shed new light on the study of stable grain-boundary atomic structures in crystalline materials.
    Language English
    Publishing date 2023-12-05
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-43536-0
    Database MEDical Literature Analysis and Retrieval System OnLINE

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