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6UBN

Crystal structure of D678E GoxA bound to glycine

Summary for 6UBN
Entry DOI10.2210/pdb6ubn/pdb
DescriptorQuinoprotein glycine oxidase, MAGNESIUM ION, SODIUM ION, ... (4 entities in total)
Functional Keywordstryotiophylquinone, oxidase, oxidoreductase
Biological sourcePseudoalteromonas luteoviolacea DSM 6061
Total number of polymer chains4
Total formula weight366519.74
Authors
Yukl, E.T. (deposition date: 2019-09-12, release date: 2019-10-23, Last modification date: 2023-10-11)
Primary citationMamounis, K.J.,Avalos, D.,Yukl, E.T.,Davidson, V.L.
Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase.
J.Biol.Chem., 294:17463-17470, 2019
Cited by
PubMed Abstract: PlGoxA from is a glycine oxidase that utilizes a protein-derived cysteine tryptophylquinone (CTQ) cofactor. A notable feature of its catalytic mechanism is that it forms a stable product-reduced CTQ adduct that is not hydrolyzed in the absence of O Asp-678 resides near the quinone moiety of PlGoxA, and an Asp is structurally conserved in this position in all tryptophylquinone enzymes. In those other enzymes, mutation of that Asp results in no or negligible CTQ formation. In this study, mutation of Asp-678 in PlGoxA did not abolish CTQ formation. This allowed, for the first time, studying the role of this residue in catalysis. D678A and D678N substitutions yielded enzyme variants with CTQ, which did not react with glycine, although glycine was present in the crystal structures in the active site. D678E PlGoxA was active but exhibited a much slower This mutation altered the kinetic mechanism of the reductive half-reaction such that one could observe a previously undetected reactive intermediate, an initial substrate-oxidized CTQ adduct, which converted to the product-reduced CTQ adduct. These results indicate that Asp-678 is involved in the initial deprotonation of the amino group of glycine, enabling nucleophilic attack of CTQ, as well as the deprotonation of the substrate-oxidized CTQ adduct, which is coupled to CTQ reduction. The structures also suggest that Asp-678 is acting as a proton relay that directs these protons to a water channel that connects the active sites on the subunits of this homotetrameric enzyme.
PubMed: 31615898
DOI: 10.1074/jbc.RA119.011255
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.15 Å)
Structure validation

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数据于2025-06-25公开中

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