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- PDB-8qvc: Deinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), wild ty... -

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Basic information

Entry
Database: PDB / ID: 8qvc
TitleDeinococcus aerius TR0125 C-glucosyl deglycosidase (CGD), wild type crystal cryoprotected with glycerol
Components
  • DUF6379 domain-containing protein
  • Xylose isomerase-like TIM barrel domain-containing protein
KeywordsLYASE / 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
Function / homology
Function and homology information


Domain of unknown function DUF6379 / C-glycoside deglycosidase beta subunit / : / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Xylose isomerase-like TIM barrel domain-containing protein / C-deglycosylation enzyme beta subunit
Similarity search - Component
Biological speciesDeinococcus aerius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFurlanetto, V. / Kalyani, D.C. / Kostelac, A. / Haltrich, D. / Hallberg, B.M. / Divne, C.
Funding support Sweden, Austria, 5items
OrganizationGrant numberCountry
Other governmentFormas 2017-00983 Sweden
Other privateOscar and Lili Lamm Memorial Foundation DO2017-0020 Sweden
Other governmentVR 2017-03877 Sweden
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: Xylose isomerase-like TIM barrel domain-containing protein
B: DUF6379 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3119
Polymers54,5242
Non-polymers7877
Water4,342241
1
A: Xylose isomerase-like TIM barrel domain-containing protein
B: DUF6379 domain-containing protein
hetero molecules

A: Xylose isomerase-like TIM barrel domain-containing protein
B: DUF6379 domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62218
Polymers109,0484
Non-polymers1,57414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9240 Å2
ΔGint-116 kcal/mol
Surface area35380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.300, 94.420, 61.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Xylose isomerase-like TIM barrel domain-containing protein


Mass: 40554.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: alpha-subunit of the alpha2beta2 heterotetramer / Source: (gene. exp.) Deinococcus aerius (bacteria) / Strain: TR0125 / Gene: DAERI_200053 / Plasmid: pNIC-CTHO / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A2I9DAN1
#2: Protein DUF6379 domain-containing protein


Mass: 13969.866 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: beta-subunit of the alpha2beta2 heterotetramer / Source: (gene. exp.) Deinococcus aerius (bacteria) / Strain: TR0125 / Gene: DAERI_200052 / Plasmid: 2A-T / Production host: Escherichia coli B (bacteria) / Strain (production host): (DE3)-T1 / References: UniProt: A0A2I9E2I0
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 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, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.953731 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 27, 2023 / Details: compound refractive lenses
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953731 Å / Relative weight: 1
ReflectionResolution: 1.8→46.15 Å / Num. obs: 50565 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 28.43 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 13.8 % / Rmerge(I) obs: 1.959 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 7446 / CC1/2: 0.617 / % possible all: 100

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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: 1.8→46.15 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 2016 3.99 %
Rwork0.1914 --
obs0.1928 50558 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 7 241 3874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083711
X-RAY DIFFRACTIONf_angle_d1.0225012
X-RAY DIFFRACTIONf_dihedral_angle_d5.849500
X-RAY DIFFRACTIONf_chiral_restr0.061532
X-RAY DIFFRACTIONf_plane_restr0.013660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.33051480.30633415X-RAY DIFFRACTION100
1.85-1.890.32311410.28413401X-RAY DIFFRACTION100
1.9-1.950.26511410.24613426X-RAY DIFFRACTION100
1.95-2.010.30031410.23343440X-RAY DIFFRACTION100
2.01-2.090.23811400.21513411X-RAY DIFFRACTION100
2.09-2.170.21781430.20833440X-RAY DIFFRACTION100
2.17-2.270.25881400.21243430X-RAY DIFFRACTION100
2.27-2.390.2171430.19633452X-RAY DIFFRACTION100
2.39-2.540.23781460.19523447X-RAY DIFFRACTION100
2.54-2.730.21561340.19563465X-RAY DIFFRACTION100
2.73-3.010.21291510.20123491X-RAY DIFFRACTION100
3.01-3.440.20961440.19273494X-RAY DIFFRACTION100
3.44-4.340.22891500.16353532X-RAY DIFFRACTION100
4.34-46.150.20521540.16713698X-RAY DIFFRACTION100

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