Domain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / : / Xylose isomerase-like TIM barrel domain-containing protein / DUF6379 domain-containing protein
Oscar and Lili Lamm Memorial Foundation DO2017-0020
Other government
VR 2017-03877
Austrian Science Fund
FWF P33545
Austria
Austrian Science Fund
FWF W1224
Austria
Citation
Journal: J Mol Biol / Year: 2024 Title: Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius. Authors: Valentina Furlanetto / Dayanand C Kalyani / Anja Kostelac / Jolanta Puc / Dietmar Haltrich / B Martin Hällberg / Christina Divne / 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 ...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).
A: Xylose isomerase-like TIM barrel domain-containing protein B: DUF6379 domain-containing protein C: Xylose isomerase-like TIM barrel domain-containing protein D: DUF6379 domain-containing protein hetero molecules
Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
Has ligand of interest
N
-
Experimental details
-
Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 1
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Sample preparation
Crystal
Density Matthews: 2.96 Å3/Da / Density % sol: 58.41 %
Crystal grow
Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES pH 7.5, 12% (w/v) polyethylene glycol 3,350, 5 mM CoCl2, 5 mM CdCl2, 5 mM MgCl2, and 5 mM NiCl2
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Data collection
Diffraction
Mean temperature: 100 K / Serial crystal experiment: N
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