7QW4

Pden_5119 protein

Summary for 7QW4

• Entry DOI: 10.2210/pdb7qw4/pdb
• Descriptor: NADPH-dependent FMN reductase (1 entity in total)
• Functional Keywords: flavinreductase, cytosolic protein
• Biological source: Paracoccus denitrificans PD1222
• Total number of polymer chains: 20
• Total formula weight: 412566.72

Authors

Kryl, M.,Sedlacek, V. (deposition date: 2022-01-24, release date: 2023-02-08, Last modification date: 2024-05-01)

Primary citation

Kryl, M.,Sedlacek, V.,Kucera, I.
Structural Insight into Catalysis by the Flavin-Dependent NADH Oxidase (Pden_5119) of Paracoccus denitrificans .
Int J Mol Sci, 24:-, 2023

PubMed Abstract: The Pden_5119 protein oxidizes NADH with oxygen under mediation by the bound flavin mononucleotide (FMN) and may be involved in the maintenance of the cellular redox pool. In biochemical characterization, the curve of the pH-rate dependence was bell-shaped with pK = 6.6 and pK = 9.2 at 2 μM FMN while it contained only a descending limb pK of 9.7 at 50 μM FMN. The enzyme was found to undergo inactivation by reagents reactive with histidine, lysine, tyrosine, and arginine. In the first three cases, FMN exerted a protective effect against the inactivation. X-ray structural analysis coupled with site-directed mutagenesis identified three amino acid residues important to the catalysis. Structural and kinetic data suggest that His-117 plays a role in the binding and positioning of the isoalloxazine ring of FMN, Lys-82 fixes the nicotinamide ring of NADH to support the -hydride transfer, and Arg-116 with its positive charge promotes the reaction between dioxygen and reduced flavin.

PubMed: 36835143
DOI: 10.3390/ijms24043732

Experimental method

X-RAY DIFFRACTION (3.1 Å)