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

Arch Biochem Biophys. 2022 Jan 15:715:109100. doi: 10.1016/j.abb.2021.109100. Epub 2021 Dec 2.

Abstract

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.

Keywords: 6-OH-FAD; Flavin N5 adduct; Flavin versatility; Ligand identity; Pseudomonas aeruginosa; d-arginine Dehydrogenase.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • 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
  • Flavin-Adenine Dinucleotide / analogs & derivatives*
  • Flavin-Adenine Dinucleotide / chemistry
  • Flavin-Adenine Dinucleotide / metabolism
  • Guanidines / chemistry*
  • Guanidines / metabolism
  • Hydrogen Bonding
  • Mutation
  • Protein Binding
  • Pseudomonas aeruginosa / enzymology
  • Static Electricity

Substances

  • Bacterial Proteins
  • Guanidines
  • Flavin-Adenine Dinucleotide
  • 6-hydroxy-FAD
  • Arginine
  • Amino Acid Oxidoreductases
  • arginine oxidase