7RDF

Crystal structure of Pseudomonas aeruginosa D-Arginine Dehydrogenase Y249F co-crystallized in the presence of D-arginine

Summary for 7RDF

• Entry DOI: 10.2210/pdb7rdf/pdb
• Descriptor: FAD-dependent catabolic D-arginine dehydrogenase DauA, [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(~{E})-4-carbamimidamidobut-2-enoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate, 6-HYDROXY-FLAVIN-ADENINE DINUCLEOTIDE, ... (6 entities in total)
• Functional Keywords: flavin versatility, flavin n5 adduct, 6-oh-fad, d-arginine dehydrogenase, ligand identity, flavoprotein
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
• Total number of polymer chains: 1
• Total formula weight: 42691.36

Authors

Reis, R.A.G.,Iyer, A.,Agniswamy, A.,Weber, I.T.,Gadda, G. (deposition date: 2021-07-09, release date: 2021-12-22, Last modification date: 2023-10-18)

Primary citation

Iyer, A.,Reis, R.A.G.,Agniswamy, J.,Weber, I.T.,Gadda, G.
Discovery of a new flavin N5-adduct in a tyrosine to phenylalanine variant of d-Arginine dehydrogenase.
Arch.Biochem.Biophys., 715:109100-109100, 2021

PubMed 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.

PubMed: 34864048
DOI: 10.1016/j.abb.2021.109100

Experimental method

X-RAY DIFFRACTION (1.29 Å)