8JT7

Structure of arginine oxidase from Pseudomonas sp. TRU 7192

Summary for 8JT7

• Entry DOI: 10.2210/pdb8jt7/pdb
• EMDB information: 36635
• Descriptor: Amine oxidoreductase, FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: Pseudomonas sp.
• Total number of polymer chains: 1
• Total formula weight: 68178.71

Authors

Yamaguchi, H.,Numoto, N.,Suzuki, H.,Nishikawa, K.,Kamegawa, A.,Takahashi, K.,Sugiki, M.,Fujiyoshi, Y. (deposition date: 2023-06-21, release date: 2024-06-26, Last modification date: 2025-01-15)

Primary citation

Yamaguchi, H.,Takahashi, K.,Numoto, N.,Suzuki, H.,Tatsumi, M.,Kamegawa, A.,Nishikawa, K.,Asano, Y.,Mizukoshi, T.,Miyano, H.,Fujiyoshi, Y.,Sugiki, M.
Open and closed structures of L-arginine oxidase by cryo-electron microscopy and X-ray crystallography.
J.Biochem., 177:27-36, 2025

PubMed Abstract: L-arginine oxidase (AROD, EC 1.4.3.25) is an oxidoreductase that catalyses the deamination of L-arginine, with flavin adenine dinucleotide (FAD) as a cofactor. Recently identified AROD from Pseudomonas sp. TPU 7192 (PT-AROD) demonstrates high selectivity for L-arginine. This enzyme is useful for accurate assays of L-arginine in biological samples. The structural characteristics of the FAD-dependent AROD, however, remain unknown. Here, we report the structure of PT-AROD at a resolution of 2.3 Å by cryo-electron microscopy. PT-AROD adopts an octameric structure with D4 symmetry, which is consistent with its molecular weight in solution, estimated by mass photometry. Comparative analysis of this structure with that determined using X-ray crystallography reveals open and closed forms of the lid-like loop at the entrance to the substrate pocket. Furthermore, mutation of Glu493, located at the substrate binding site, diminishes substrate selectivity, suggesting that this residue contributes significantly to the high selectivity of PT-AROD.

PubMed: 39420599
DOI: 10.1093/jb/mvae070

Experimental method

ELECTRON MICROSCOPY (2.34 Å)