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- PDB-8qve: C-glucosyl oxidoreductase (DaCGO1) from Deinococcus aerius -

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Basic information

Entry
Database: PDB / ID: 8qve
TitleC-glucosyl oxidoreductase (DaCGO1) from Deinococcus aerius
ComponentsPyranose oxidase
KeywordsLYASE / bacterial C-glycosyl oxidoreductase / C-C bond cleavage / C-glucosyl aromatic polyketides / C-glucosyl flavonoids / Deinococcus aerius / soil bacterium / GMC oxidoreductase
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / flavin adenine dinucleotide binding
Similarity search - Function
Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / : / FLAVIN-ADENINE DINUCLEOTIDE / Pyranose oxidase
Similarity search - Component
Biological speciesDeinococcus aerius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFurlanetto, V. / Kalyani, D.C. / Kostelac, A. / Haltrich, D. / Hallberg, B.M. / Divne, C.
Funding support Austria, 5items
OrganizationGrant numberCountry
Other governmentFormas 2017-00983
Other privateOscar and Lili Lamm Memorial Foundation DO2017-0020
Other governmentVR 2017-03877
Austrian Science FundFWF P33545 Austria
Austrian Science FundFWF W1224 Austria
CitationJournal: 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).
History
DepositionOct 17, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyranose oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1519
Polymers52,7381
Non-polymers1,4128
Water4,972276
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Monomer confirmed by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-29 kcal/mol
Surface area18470 Å2
Unit cell
Length a, b, c (Å)84.980, 123.710, 99.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-605-

CD

21A-907-

HOH

31A-927-

HOH

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Components

#1: Protein Pyranose oxidase


Mass: 52738.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus aerius (bacteria) / Gene: DAERI_200051 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A2I9D0D5
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M CdCl2, 0.1 M sodium acetate pH 4.6, 30% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.91788 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 9, 2022 / Details: compound refractive lenses
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91788 Å / Relative weight: 1
ReflectionResolution: 1.7→49.59 Å / Num. obs: 57611 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.153 / Net I/σ(I): 13.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.54 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8961 / CC1/2: 0.733

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→49.59 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2148 2000 3.47 %
Rwork0.1893 --
obs0.1902 57607 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→49.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3711 0 69 276 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083895
X-RAY DIFFRACTIONf_angle_d0.9215335
X-RAY DIFFRACTIONf_dihedral_angle_d10.735547
X-RAY DIFFRACTIONf_chiral_restr0.058589
X-RAY DIFFRACTIONf_plane_restr0.01711
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.32591400.28433909X-RAY DIFFRACTION100
1.74-1.790.28731410.26693919X-RAY DIFFRACTION100
1.79-1.840.28011420.25623937X-RAY DIFFRACTION100
1.84-1.90.30821400.24423899X-RAY DIFFRACTION100
1.9-1.970.26611430.2353976X-RAY DIFFRACTION100
1.97-2.050.24751410.2073917X-RAY DIFFRACTION100
2.05-2.140.26331430.20253994X-RAY DIFFRACTION100
2.14-2.250.25071420.2023934X-RAY DIFFRACTION100
2.25-2.40.24961420.19293947X-RAY DIFFRACTION100
2.4-2.580.20961430.19253990X-RAY DIFFRACTION100
2.58-2.840.24541440.19473969X-RAY DIFFRACTION100
2.84-3.250.21211440.18814006X-RAY DIFFRACTION100
3.25-4.10.16961450.16624028X-RAY DIFFRACTION100
4.1-49.590.15681500.15334182X-RAY DIFFRACTION100

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