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- PDB-7exb: DfgA-DfgB complex apo 2.4 angstrom -

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Basic information

Entry
Database: PDB / ID: 7exb
TitleDfgA-DfgB complex apo 2.4 angstrom
Components
  • DfgB
  • Sugar phosphate isomerase/epimerase
KeywordsLYASE / C-deglycosylation / sugar phosphate isomerase/epimerase
Function / homologyDomain of unknown function DUF6379 / Domain of unknown function (DUF6379) / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / isomerase activity / : / DUF6379 domain-containing protein / Sugar phosphate isomerase/epimerase
Function and homology information
Biological species[Eubacterium] cellulosolvens 6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMori, T. / Senda, M. / Senda, T. / Abe, I.
CitationJournal: Nat Commun / Year: 2021
Title: C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes.
Authors: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi ...Authors: Takahiro Mori / Takuto Kumano / Haibing He / Satomi Watanabe / Miki Senda / Toshio Moriya / Naruhiko Adachi / Sanae Hori / Yuzu Terashita / Masato Kawasaki / Yoshiteru Hashimoto / Takayoshi Awakawa / Toshiya Senda / Ikuro Abe / Michihiko Kobayashi /
Abstract: C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and ...C-Glycosides, in which a sugar moiety is linked via a carbon-carbon (C-C) bond to a non-sugar moiety (aglycone), are found in our food and medicine. The C-C bond is cleaved by intestinal microbes and the resulting aglycones exert various bioactivities. Although the enzymes responsible for the reactions have been identified, their catalytic mechanisms and the generality of the reactions in nature remain to be explored. Here, we present the identification and structural basis for the activation of xenobiotic C-glycosides by heterocomplex C-deglycosylation enzymes from intestinal and soil bacteria. They are found to be metal-dependent enzymes exhibiting broad substrate specificity toward C-glycosides. X-ray crystallographic and cryo-electron microscopic analyses, as well as structure-based mutagenesis, reveal the structural details of these enzymes and the detailed catalytic mechanisms of their remarkable C-C bond cleavage reactions. Furthermore, bioinformatic and biochemical analyses suggest that the C-deglycosylation enzymes are widely distributed in the gut, soil, and marine bacteria.
History
DepositionMay 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sugar phosphate isomerase/epimerase
B: DfgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6627
Polymers52,2222
Non-polymers4395
Water5,927329
1
A: Sugar phosphate isomerase/epimerase
B: DfgB
hetero molecules

A: Sugar phosphate isomerase/epimerase
B: DfgB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,32314
Polymers104,4454
Non-polymers87810
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area9690 Å2
ΔGint-156 kcal/mol
Surface area36100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.970, 138.970, 227.028
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422
Space group name HallP642(x,y,z+1/6)
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z
#9: y,x,-z+1/3
#10: -y,-x,-z+1/3
#11: -x+y,y,-z
#12: x,x-y,-z+2/3

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Components

#1: Protein Sugar phosphate isomerase/epimerase / DfgA


Mass: 33764.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] cellulosolvens 6 (bacteria)
Gene: EubceDRAFT1_2664 / Production host: Escherichia coli (E. coli) / References: UniProt: I5AX50
#2: Protein DfgB


Mass: 18458.150 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Eubacterium] cellulosolvens 6 (bacteria)
Gene: EubceDRAFT1_2663 / Production host: Escherichia coli (E. coli) / References: UniProt: I5AX49
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 6.06 Å3/Da / Density % sol: 79.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM Tris-HCl (pH8.5), 1190 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.88 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.88 Å / Relative weight: 1
ReflectionResolution: 2.4→47.1 Å / Num. obs: 51290 / % possible obs: 100 % / Redundancy: 36.9 % / Biso Wilson estimate: 43.75 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.14 / Net I/σ(I): 27.4
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 22.8 % / Rmerge(I) obs: 1.417 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 4359 / CC1/2: 0.83 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BVS

7bvs


Resolution: 2.4→47.1 Å / SU ML: 0.2941 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.203 2578 5.03 %
Rwork0.1778 48653 -
obs0.179 51231 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3559 0 21 329 3909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753679
X-RAY DIFFRACTIONf_angle_d0.89934988
X-RAY DIFFRACTIONf_chiral_restr0.0559526
X-RAY DIFFRACTIONf_plane_restr0.0072639
X-RAY DIFFRACTIONf_dihedral_angle_d5.9304482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.36831480.312626X-RAY DIFFRACTION99.86
2.45-2.50.31181480.26882644X-RAY DIFFRACTION99.96
2.5-2.550.27711320.24682646X-RAY DIFFRACTION100
2.55-2.610.25581760.21672661X-RAY DIFFRACTION100
2.61-2.670.24141530.21222629X-RAY DIFFRACTION100
2.68-2.750.26161580.20842622X-RAY DIFFRACTION100
2.75-2.830.24271370.21972702X-RAY DIFFRACTION100
2.83-2.920.25571400.22542643X-RAY DIFFRACTION100
2.92-3.020.28481370.22912701X-RAY DIFFRACTION100
3.02-3.140.22351240.21122681X-RAY DIFFRACTION100
3.14-3.290.2411340.19972685X-RAY DIFFRACTION100
3.29-3.460.2081540.18352687X-RAY DIFFRACTION100
3.46-3.680.23851320.18662718X-RAY DIFFRACTION100
3.68-3.960.17381390.16722718X-RAY DIFFRACTION100
3.96-4.360.12971360.13332747X-RAY DIFFRACTION100
4.36-4.990.12861460.11992736X-RAY DIFFRACTION100
4.99-6.280.18081500.15562806X-RAY DIFFRACTION100
6.29-47.10.1821340.1543001X-RAY DIFFRACTION99.97

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