7DVE

Crystal structure of FAD-dependent C-glycoside oxidase

Summary for 7DVE

• Entry DOI: 10.2210/pdb7dve/pdb
• Descriptor: 6'''-hydroxyparomomycin C oxidase, FLAVIN-ADENINE DINUCLEOTIDE, SULFATE ION, ... (4 entities in total)
• Functional Keywords: fad-dependent c-glycoside oxidase, oxidoreductase
• Biological source: Microbacterium trichothecenolyticum
• Total number of polymer chains: 2
• Total formula weight: 113546.90

Authors

Senda, M.,Watanabe, S.,Kumano, T.,Kobayashi, M.,Senda, T. (deposition date: 2021-01-13, release date: 2021-09-08, Last modification date: 2023-11-29)

Primary citation

Kumano, T.,Hori, S.,Watanabe, S.,Terashita, Y.,Yu, H.Y.,Hashimoto, Y.,Senda, T.,Senda, M.,Kobayashi, M.
FAD-dependent C -glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis.
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: -glycosides have a unique structure, in which an anomeric carbon of a sugar is directly bonded to the carbon of an aglycone skeleton. One of the natural -glycosides, carminic acid, is utilized by the food, cosmetic, and pharmaceutical industries, for a total of more than 200 tons/y worldwide. However, a metabolic pathway of carminic acid has never been identified. In this study, we isolated the previously unknown carminic acid-catabolizing microorganism and discovered a flavoenzyme "-glycoside 3-oxidase" named CarA that catalyzes oxidation of the sugar moiety of carminic acid. A Basic Local Alignment Search Tool (BLAST) search demonstrated that CarA homologs were distributed in soil microorganisms but not intestinal ones. In addition to CarA, two CarA homologs were cloned and heterologously expressed, and their biochemical properties were determined. Furthermore, a crystal structure of one homolog was determined. Together with the biochemical analysis, the crystal structure and a mutagenesis analysis of CarA revealed the mechanisms underlying their substrate specificity and catalytic reaction. Our study suggests that CarA and its homologs play a crucial role in the metabolism of -glycosides in nature.

PubMed: 34583991
DOI: 10.1073/pnas.2106580118

Experimental method

X-RAY DIFFRACTION (2.4 Å)