7RF9

O2-, PLP-dependent desaturase Plu4 intermediate-bound enzyme

Summary for 7RF9

• Entry DOI: 10.2210/pdb7rf9/pdb
• Related: 7N79
• Descriptor: Aminotran_1_2 domain-containing protein, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ACETATE ION, ... (8 entities in total)
• Functional Keywords: arginine desaturase, oxygen- and plp-dependent oxidase, fold type i, biosynthesis, biosynthetic protein
• Biological source: Pseudoalteromonas luteoviolacea
• Total number of polymer chains: 4
• Total formula weight: 182916.96

Authors

Hoffarth, E.R.,Ryan, K.S. (deposition date: 2021-07-13, release date: 2021-10-06, Last modification date: 2023-10-18)

Primary citation

Hoffarth, E.R.,Caddell Haatveit, K.,Kuatsjah, E.,MacNeil, G.A.,Saroya, S.,Walsby, C.J.,Eltis, L.D.,Houk, K.N.,Garcia-Borras, M.,Ryan, K.S.
A shared mechanistic pathway for pyridoxal phosphate-dependent arginine oxidases.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: The mechanism by which molecular oxygen is activated by the organic cofactor pyridoxal phosphate (PLP) for oxidation reactions remains poorly understood. Recent work has identified arginine oxidases that catalyze desaturation or hydroxylation reactions. Here, we investigate a desaturase from the indolmycin pathway. Our work, combining X-ray crystallographic, biochemical, spectroscopic, and computational studies, supports a shared mechanism with arginine hydroxylases, involving two rounds of single-electron transfer to oxygen and superoxide rebound at the 4' carbon of the PLP cofactor. The precise positioning of a water molecule in the active site is proposed to control the final reaction outcome. This proposed mechanism provides a unified framework to understand how oxygen can be activated by PLP-dependent enzymes for oxidation of arginine and elucidates a shared mechanistic pathway and intertwined evolutionary history for arginine desaturases and hydroxylases.

PubMed: 34580201
DOI: 10.1073/pnas.2012591118

Experimental method

X-RAY DIFFRACTION (1.926 Å)