Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural and Functional Characterization of a Gene Cluster Responsible for Deglycosylation of C-glucosyl Flavonoids and Xanthonoids by Deinococcus aerius.
Journal, issue, pages	J Mol Biol, Vol. 436, Issue 9, Page 168547, Year 2024
Publish date	May 1, 2024
Authors	Valentina Furlanetto / Dayanand C Kalyani / Anja Kostelac / Jolanta Puc / Dietmar Haltrich / B Martin Hällberg / Christina Divne /
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 ...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).
External links	J Mol Biol / PubMed:38508304
Methods	EM (single particle) / X-ray diffraction
Resolution	1.7 - 3.3 Å
Structure data	42375 8umc EMDB-42375, PDB-8umc: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), cryo-EM Method: EM (single particle) / Resolution: 2.5 Å PDB-8qvc: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), wild type crystal cryoprotected with glycerol Method: X-RAY DIFFRACTION / Resolution: 1.8 Å PDB-8qvd: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), wild type crystal cryoprotected with glycerol Method: X-RAY DIFFRACTION / Resolution: 3.3 Å PDB-8qve: C-glucosyl oxidoreductase (DaCGO1) from Deinococcus aerius Method: X-RAY DIFFRACTION / Resolution: 1.7 Å
Chemicals	ChemComp-CD: Unknown entry ChemComp-HOH: WATER ChemComp-FAD: FLAVIN-ADENINE DINUCLEOTIDE / FADYM ChemComp-ACT: ACETATE ION ChemComp-MN*: Unknown entry
Source	deinococcus aerius (bacteria)
Keywords	LYASE / 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 / bacterial C-glycosyl oxidoreductase / GMC oxidoreductase