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- PDB-7bvs: DfgA-DfgB complex apo -

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Basic information

Entry
Database: PDB / ID: 7bvs
TitleDfgA-DfgB complex apo
Components
  • DfgB
  • Sugar phosphate isomerase/epimerase
KeywordsLYASE / C-deglycosylation / sugar phosphate isomerase/epimerase
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Other carbon-carbon lyases / lyase activity / metal ion binding
Similarity search - Function
Domain of unknown function DUF6379 / C-glycoside deglycosidase beta subunit / : / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / C-glycoside deglycosidase beta subunit / C-glycoside deglycosidase alpha subunit
Similarity search - Component
Biological species[Eubacterium] cellulosolvens 6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsMori, T. / He, H. / Abe, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 17, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Experimental preparation / Refinement description / Structure summary
Category: atom_site / database_2 ...atom_site / database_2 / exptl_crystal_grow / pdbx_audit_support / pdbx_contact_author / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_conn / struct_mon_prot_cis / struct_sheet_range
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pdbx_details / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_low / _refine_ls_restr.dev_ideal / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.percent_reflns_obs / _software.name / _software.version / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id
Description: Occupancy of atoms on special symmetry positions
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 26, 2022Group: 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 2.2Nov 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)52,6587
Polymers52,2222
Non-polymers4355
Water181
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)105,31514
Polymers104,4454
Non-polymers87010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area10270 Å2
ΔGint-122 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.213, 138.213, 227.001
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

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Protein , 2 types, 2 molecules AB

#1: Protein Sugar phosphate isomerase/epimerase


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 BL21 (bacteria) / 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 BL21 (bacteria) / References: UniProt: I5AX49

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Non-polymers , 4 types, 6 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: 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
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 6.13 Å3/Da / Density % sol: 79.92 %
Crystal growTemperature: 313 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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→46.94 Å / Num. obs: 30686 / % possible obs: 100 % / Redundancy: 20.1 % / Biso Wilson estimate: 51.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 24.3
Reflection shellResolution: 2.85→3 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 4392 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DRE

7dre


Resolution: 2.85→45.24 Å / SU ML: 0.3888 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.4171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2333 2000 6.53 %
Rwork0.1984 28631 -
obs0.2007 30631 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.25 Å2
Refinement stepCycle: LAST / Resolution: 2.85→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 22 1 3607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943696
X-RAY DIFFRACTIONf_angle_d0.99425003
X-RAY DIFFRACTIONf_chiral_restr0.0553525
X-RAY DIFFRACTIONf_plane_restr0.0079641
X-RAY DIFFRACTIONf_dihedral_angle_d17.31041373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.43441400.32242004X-RAY DIFFRACTION100
2.92-30.37111390.28991992X-RAY DIFFRACTION100
3-3.090.33551400.26892002X-RAY DIFFRACTION100
3.09-3.190.33741400.26672001X-RAY DIFFRACTION100
3.19-3.30.33451400.26242008X-RAY DIFFRACTION100
3.3-3.430.28221410.24592014X-RAY DIFFRACTION100
3.43-3.590.25261400.22272012X-RAY DIFFRACTION100
3.59-3.780.24741420.20182024X-RAY DIFFRACTION100
3.78-4.020.21521420.18622041X-RAY DIFFRACTION100
4.02-4.330.20631430.16842047X-RAY DIFFRACTION100
4.33-4.760.16671430.14832049X-RAY DIFFRACTION100
4.76-5.450.18861450.16082076X-RAY DIFFRACTION100
5.45-6.860.21731480.17592109X-RAY DIFFRACTION100
6.86-45.240.16811570.16352252X-RAY DIFFRACTION99.71

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