6A1L
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and benzoic acid
Summary for 6A1L
| Entry DOI | 10.2210/pdb6a1l/pdb |
| Descriptor | 4-hydroxymandelate oxidase, 1-deoxy-1-(7,8-dimethyl-2,4-dioxo-3,4-dihydropyrimido[4,5-b]quinolin-10(2H)-yl)-5-O-phosphono-D-ribitol, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | fmn-dependent oxidase, flavoprotein |
| Biological source | Amycolatopsis orientalis (Nocardia orientalis) |
| Total number of polymer chains | 1 |
| Total formula weight | 40753.46 |
| Authors | |
| Primary citation | Lyu, S.Y.,Lin, K.H.,Yeh, H.W.,Li, Y.S.,Huang, C.M.,Wang, Y.L.,Shih, H.W.,Hsu, N.S.,Wu, C.J.,Li, T.L. The flavin mononucleotide cofactor in alpha-hydroxyacid oxidases exerts its electrophilic/nucleophilic duality in control of the substrate-oxidation level. Acta Crystallogr D Struct Biol, 75:918-929, 2019 Cited by PubMed Abstract: The Y128F single mutant of p-hydroxymandelate oxidase (Hmo) is capable of oxidizing mandelate to benzoate via a four-electron oxidative decarboxylation reaction. When benzoylformate (the product of the first two-electron oxidation) and hydrogen peroxide (an oxidant) were used as substrates the reaction did not proceed, suggesting that free hydrogen peroxide is not the committed oxidant in the second two-electron oxidation. How the flavin mononucleotide (FMN)-dependent four-electron oxidation reaction takes place remains elusive. Structural and biochemical explorations have shed new light on this issue. 15 high-resolution crystal structures of Hmo and its mutants liganded with or without a substrate reveal that oxidized FMN (FMN) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMN to a nucleophilic ylide, which is in a position to act on an α-ketoacid, forming an N5-acyl-FMN dead-end adduct. In four-electron oxidation, an intramolecular disproportionation reaction via an N5-alkanol-FMN C'α carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMN cofactor in combination with an α-hydroxyamide or α-ketoamide biochemically and structurally supports the proposed mechanism. PubMed: 31588923DOI: 10.1107/S2059798319011938 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.4 Å) |
Structure validation
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