8QVD

Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), wild type crystal cryoprotected with glycerol

Summary for 8QVD

• Entry DOI: 10.2210/pdb8qvd/pdb
• Descriptor: Xylose isomerase-like TIM barrel domain-containing protein, DUF6379 domain-containing protein, CADMIUM ION (3 entities in total)
• Functional Keywords: bacterial c-glucosyl deglycosidase, c-c bond cleavage, c-glucosyl aromatic polyketides, c-glucosyl flavonoids, deinococcus aerius, soil bacterium, n-terminal duf6379 beta-sandwich domain, c-terminal tim-barrel domain, alpha2beta2 heterotetramer, lyase
• Biological source: Deinococcus aerius; More
• Total number of polymer chains: 4
• Total formula weight: 110734.55

Authors

Furlanetto, V.,Kalyani, D.C.,Kostelac, A.,Haltrich, D.,Hallberg, B.M.,Divne, C. (deposition date: 2023-10-17, release date: 2024-05-29)

Primary citation

Furlanetto, V.,Kalyani, D.C.,Kostelac, A.,Puc, J.,Haltrich, D.,Hallberg, B.M.,Divne, C.
Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius.
J.Mol.Biol., 436:168547-168547, 2024

PubMed Abstract: Plant C-glycosylated aromatic polyketides are important for plant and animal health. These are specialized metabolites that perform functions both within the plant, and in interaction with soil or intestinal microbes. Despite the importance of these plant compounds, there is still limited knowledge of how they are metabolized. The Gram-positive aerobic soil bacterium Deinococcus aerius strain TR0125 and other Deinococcus species thrive in a wide range of harsh environments. In this work, we identified a C-glycoside deglycosylation gene cluster in the genome of D. aerius. The cluster includes three genes coding for a GMC-type oxidoreductase (DaCGO1) that oxidizes the glucosyl C3 position in aromatic C-glucosyl compounds, which in turn provides the substrate for the C-glycoside deglycosidase (DaCGD; composed of α+β subunits) that cleaves the glucosyl-aglycone C-C bond. Our results from size-exclusion chromatography, single particle cryo-electron microscopy and X-ray crystallography show that DaCGD is an αβ heterotetramer, which represents a novel oligomeric state among bacterial CGDs. Importantly, the high-resolution X-ray structure of DaCGD provides valuable insights into the activation of the catalytic hydroxide ion by Lys261. DaCGO1 is specific for the 6-C-glucosyl flavones isovitexin, isoorientin and the 2-C-glucosyl xanthonoid mangiferin, and the subsequent C-C-bond cleavage by DaCGD generated apigenin, luteolin and norathyriol, respectively. Of the substrates tested, isovitexin was the preferred substrate (DaCGO1, K 0.047 mM, k 51 min; DaCGO1/DaCGD, K 0.083 mM, k 0.42 min).

PubMed: 38508304
DOI: 10.1016/j.jmb.2024.168547

Experimental method

X-RAY DIFFRACTION (3.3 Å)