Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase

• Published in: Archives of biochemistry and biophysics 2022-01, Vol.715 (C), p.109100-109100, Article 109100
• Main Authors: Iyer, Archana, Reis, Renata A.G., Agniswamy, Johnson, Weber, Irene T., Gadda, Giovanni
• Format: Article
• Language: English
• Subjects: 6-OH-FAD; Amino Acid Oxidoreductases - chemistry; Amino Acid Oxidoreductases - genetics; Amino Acid Oxidoreductases - metabolism; Arginine - chemistry; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalytic Domain; Crystallography, X-Ray; d-arginine Dehydrogenase; Flavin N5 adduct; Flavin versatility; Flavin-Adenine Dinucleotide - analogs & derivatives; Flavin-Adenine Dinucleotide - chemistry; Flavin-Adenine Dinucleotide - metabolism; Guanidines - chemistry; Guanidines - metabolism; Hydrogen Bonding; Ligand identity; Mutation; Protein Binding; Pseudomonas aeruginosa; Pseudomonas aeruginosa - enzymology; Static Electricity
• ISSN: 0003-9861; 1096-0384
• DOI: 10.1016/j.abb.2021.109100

d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) catalyzes the flavin-dependent oxidation of d-arginine and other d-amino acids. Here, we report the crystal structure at 1.29 Å resolution for PaDADH-Y249F expressed and co-crystallized with d-arginine. The overall structure of PaDADH-Y249F resembled PaDADH-WT, but the electron density for the flavin cofactor was ambiguous, suggesting the presence of modified flavins. Electron density maps and mass spectrometric analysis confirmed the presence of both N5-(4-guanidino-oxobutyl)-FAD and 6-OH-FAD in a single crystal of PaDADH-Y249F and helped with the further refinement of the X-ray crystal structure. The versatility of the reduced flavin is apparent in the PaDADH-Y249F structure and is evidenced by the multiple functions it can perform in the same active site. [Display omitted]