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- PDB-8ai6: Crystal structure of radical SAM epimerase EpeE D210A mutant from... -

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Basic information

Entry
Database: PDB / ID: 8ai6
TitleCrystal structure of radical SAM epimerase EpeE D210A mutant from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and persulfurated cysteine bound
ComponentsPutative peptide biosynthesis protein YydG
KeywordsMETAL BINDING PROTEIN / radical SAM / metalloenzyme / iron-sulfur / RiPP
Function / homology
Function and homology information


catalytic activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Peptide radical SAM maturase , YydG / : / 4Fe-4S single cluster domain / Radical SAM superfamily / Radical SAM core domain profile. / Radical SAM / Aldolase-type TIM barrel
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / S-ADENOSYL-L-HOMOCYSTEINE / IRON/SULFUR CLUSTER / Putative peptide biosynthesis protein YydG
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPolsinelli, I. / Legrand, P. / Fyfe, C.D. / Benjdia, A. / Berteau, O.
Funding support France, European Union, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0014 France
European Research Council (ERC)617053European Union
Citation
Journal: Nat.Chem.Biol. / Year: 2024
Title: Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme.
Authors: Kubiak, X. / Polsinelli, I. / Chavas, L.M.G. / Fyfe, C.D. / Guillot, A. / Fradale, L. / Brewee, C. / Grimaldi, S. / Gerbaud, G. / Thureau, A. / Legrand, P. / Berteau, O. / Benjdia, A.
#1: Journal: Nat Chem / Year: 2017
Title: Post-translational modification of ribosomally synthesized peptides by a radical SAM epimerase in Bacillus subtilis.
Authors: Benjdia, A. / Guillot, A. / Ruffie, P. / Leprince, J. / Berteau, O.
History
DepositionJul 25, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 13, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative peptide biosynthesis protein YydG
B: Putative peptide biosynthesis protein YydG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,49229
Polymers79,8812
Non-polymers3,61127
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.82, 92.25, 127.08
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative peptide biosynthesis protein YydG


Mass: 39940.500 Da / Num. of mol.: 2 / Mutation: D210A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yydG, BSU40170 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q45595

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Non-polymers , 5 types, 414 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / Details: 15% (w/v) PEG 1000, 100 mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationMonochromator: channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→48.7 Å / Num. obs: 962748 / % possible obs: 100 % / Redundancy: 14.7 % / CC1/2: 0.975 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.036 / Rrim(I) all: 0.135 / Net I/σ(I): 13.1
Reflection shellResolution: 1.95→2 Å / Rmerge(I) obs: 2.032 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 74413 / CC1/2: 0.566 / Rpim(I) all: 0.532 / Rrim(I) all: 2.101

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
MxCuBE2.1data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fe-SAD experimental model

Resolution: 1.95→48.7 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.14 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.2117 3282 -RANDOM
Rwork0.1901 ---
obs0.1912 65639 100 %-
Displacement parametersBiso mean: 51.69 Å2
Baniso -1Baniso -2Baniso -3
1--3.0644 Å20 Å20 Å2
2--8.8579 Å20 Å2
3----5.7935 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 1.95→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5296 0 177 387 5860
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085744HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.937750HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2043SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes974HARMONIC5
X-RAY DIFFRACTIONt_it5744HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion731SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5271SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion16.72
LS refinement shellResolution: 1.95→1.96 Å
RfactorNum. reflection% reflection
Rfree0.3077 65 -
Rwork0.3085 --
obs--100 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.26570.4272-0.43851.1598-0.08140.8830.0254-0.0442-0.0084-0.0442-0.0869-0.0476-0.0084-0.04760.0615-0.23160.0481-0.0256-0.08860.0203-0.18291.3247-13.95-23.1323
22.4248-0.43050.96081.4552-0.05531.56540.1355-0.12610.1058-0.1261-0.08510.06930.10580.0693-0.0503-0.19350.03760.0254-0.0157-0.0259-0.120931.7134-26.4498-22.359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-4 - 317
2X-RAY DIFFRACTION1{ A|* }A401 - 505
3X-RAY DIFFRACTION1{ A|* }A601 - 804
4X-RAY DIFFRACTION2{ B|* }B-5 - 317
5X-RAY DIFFRACTION2{ B|* }B401 - 516
6X-RAY DIFFRACTION2{ B|* }B601 - 783

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