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      X-ray structure of the direct electron transfer-type FAD glucose dehydrogenase catalytic subunit complexed with a hitchhiker protein

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          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.

          Abstract

          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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          Structural analysis of fungus-derived FAD glucose dehydrogenase

          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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            Structure of fumarate reductase from Wolinella succinogenes at 2.2 A resolution.

            Fumarate reductase couples the reduction of fumarate to succinate to the oxidation of quinol to quinone, in a reaction opposite to that catalysed by the related complex II of the respiratory chain (succinate dehydrogenase). Here we describe the crystal structure at 2.2 A resolution of the three protein subunits containing fumarate reductase from the anaerobic bacterium Wolinella succinogenes. Subunit A contains the site of fumarate reduction and a covalently bound flavin adenine dinucleotide prosthetic group. Subunit B contains three iron-sulphur centres. The menaquinol-oxidizing subunit C consists of five membrane-spanning, primarily helical segments and binds two haem b molecules. On the basis of the structure, we propose a pathway of electron transfer from the dihaem cytochrome b to the site of fumarate reduction and a mechanism of fumarate reduction. The relative orientations of the soluble and membrane-embedded subunits of succinate:quinone oxidoreductases appear to be unique.
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              The 1.6 Å Crystal Structure of Pyranose Dehydrogenase from Agaricus meleagris Rationalizes Substrate Specificity and Reveals a Flavin Intermediate

              Pyranose dehydrogenases (PDHs) are extracellular flavin-dependent oxidoreductases secreted by litter-decomposing fungi with a role in natural recycling of plant matter. All major monosaccharides in lignocellulose are oxidized by PDH at comparable yields and efficiencies. Oxidation takes place as single-oxidation or sequential double-oxidation reactions of the carbohydrates, resulting in sugar derivatives oxidized primarily at C2, C3 or C2/3 with the concomitant reduction of the flavin. A suitable electron acceptor then reoxidizes the reduced flavin. Whereas oxygen is a poor electron acceptor for PDH, several alternative acceptors, e.g., quinone compounds, naturally present during lignocellulose degradation, can be used. We have determined the 1.6-Å crystal structure of PDH from Agaricus meleagris. Interestingly, the flavin ring in PDH is modified by a covalent mono- or di-atomic species at the C(4a) position. Under normal conditions, PDH is not oxidized by oxygen; however, the related enzyme pyranose 2-oxidase (P2O) activates oxygen by a mechanism that proceeds via a covalent flavin C(4a)-hydroperoxide intermediate. Although the flavin C(4a) adduct is common in monooxygenases, it is unusual for flavoprotein oxidases, and it has been proposed that formation of the intermediate would be unfavorable in these oxidases. Thus, the flavin adduct in PDH not only shows that the adduct can be favorably accommodated in the active site, but also provides important details regarding the structural, spatial and physicochemical requirements for formation of this flavin intermediate in related oxidases. Extensive in silico modeling of carbohydrates in the PDH active site allowed us to rationalize the previously reported patterns of substrate specificity and regioselectivity. To evaluate the regioselectivity of D-glucose oxidation, reduction experiments were performed using fluorinated glucose. PDH was rapidly reduced by 3-fluorinated glucose, which has the C2 position accessible for oxidation, whereas 2-fluorinated glucose performed poorly (C3 accessible), indicating that the glucose C2 position is the primary site of attack.
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                Author and article information

                Journal
                Acta Crystallogr D Struct Biol
                Acta Crystallogr D Struct Biol
                Acta Cryst. D
                Acta Crystallographica. Section D, Structural Biology
                International Union of Crystallography
                2059-7983
                01 September 2019
                28 August 2019
                28 August 2019
                : 75
                : Pt 9 ( publisher-idID: d190900 )
                : 841-851
                Affiliations
                [a ]Life Science Research Center and Faculty of Medicine, Kagawa University , 1750-1 Ikenobe, Miki-cho, Kita-gun, Kagawa 761-0793, Japan
                [b ]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
                [c ]Department of Chemistry, Missouri State University , Springfield, MO 65897, USA
                [d ]Research Center for Functional Materials, National Institute for Materials Science (NIMS) , 1-2-1 Sengen, Tsukuba, Ibaraki 305-0047, Japan
                [e ]Department of Applied Chemistry and Biochemical Engineering, Shizuoka University , 3-5-1 Johoku, Naka-ku, Hamamatsu, Shizuoka 432-8561, Japan
                [f ]Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University , Chapel Hill, NC 27599, USA
                Author notes
                Correspondence e-mail: ksode@ 123456email.unc.edu
                Author information
                https://orcid.org/0000-0003-2136-8042
                https://orcid.org/0000-0003-1424-4367
                https://orcid.org/0000-0002-3950-3372
                Article
                dw5200 ACSDAD S2059798319010878
                10.1107/S2059798319010878
                6719666
                31478907
                8d42593a-6ceb-4c61-95ff-9a163c1b7b02
                © Yoshida et al. 2019

                This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.

                History
                : 01 May 2019
                : 02 August 2019
                Page count
                Pages: 11
                Funding
                Funded by: Japan Society for the Promotion of Science
                Award ID: JP16H04175
                Award Recipient : Koji Sode
                This work was funded by Japan Society for the Promotion of Science grant JP16H04175 to Koji Sode.
                Categories
                Research Papers

                direct electron transfer,flavin adenine dinucleotide-dependent dehydrogenase complex,glucose dehydrogenase,iron–sulfur cluster,hitchhiker protein,glucose sensors,burkholderia cepacia

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