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TitleOpen and closed structures of L-arginine oxidase by cryo-electron microscopy and X-ray crystallography.
Journal, issue, pagesJ Biochem, Vol. 177, Issue 1, Page 27-36, Year 2025
Publish dateOct 18, 2024
AuthorsHiroki Yamaguchi / Kazutoshi Takahashi / Nobutaka Numoto / Hiroshi Suzuki / Moemi Tatsumi / Akiko Kamegawa / Kouki Nishikawa / Yasuhisa Asano / Toshimi Mizukoshi / Hiroshi Miyano / Yoshinori Fujiyoshi / Masayuki Sugiki /
PubMed AbstractL-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 ...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.
External linksJ Biochem / PubMed:39420599 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.34 - 3.4 Å
Structure data

36635

8jt7

EMDB-36635, PDB-8jt7:
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Method: EM (single particle) / Resolution: 2.34 Å

PDB-8t8a:
Structure of arginine oxidase from Pseudomonas sp. TRU 7192
Method: X-RAY DIFFRACTION / Resolution: 3.4 Å

Chemicals

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM

ChemComp-HOH:
WATER

Source
  • pseudomonas sp. (bacteria)
KeywordsOXIDOREDUCTASE / oxidase / arginine oxidase

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