6A1P image
Entry Detail
PDB ID:
6A1P
Keywords:
Title:
Mandelate oxidase mutant-Y128F with 5-deazariboflavin mononucleotide and phenylpyruvic acid
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2018-06-07
Release Date:
2019-06-19
Method Details:
Experimental Method:
Resolution:
1.51 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
I 4 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:4-hydroxymandelate oxidase
Mutations:Y128F
Chain IDs:A
Chain Length:377
Number of Molecules:1
Biological Source:Amycolatopsis orientalis
Primary Citation
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)
PMID: 31588923 DOI: 10.1107/S2059798319011938

Abstact

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 (FMNox) possesses a previously unknown electrophilic/nucleophilic duality. In the Y128F mutant the active-site perturbation ensemble facilitates the polarization of FMNox to a nucleophilic ylide, which is in a position to act on an α-ketoacid, forming an N5-acyl-FMNred dead-end adduct. In four-electron oxidation, an intramolecular disproportionation reaction via an N5-alkanol-FMNred C'α carbanion intermediate may account for the ThDP/PLP/NADPH-independent oxidative decarboxylation reaction. A synthetic 5-deaza-FMNox cofactor in combination with an α-hydroxyamide or α-ketoamide biochemically and structurally supports the proposed mechanism.

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