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- PDB-8ai1: Crystal structure of radical SAM epimerase EpeE from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 8ai1
TitleCrystal structure of radical SAM epimerase EpeE from Bacillus subtilis with [4Fe-4S] clusters and S-adenosyl-L-homocysteine 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: 2.4 Å
AuthorsKubiak, X. / Polsinelli, I. / Chavas, L.M.G. / 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

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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)83,52427
Polymers79,9052
Non-polymers3,61925
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint-43 kcal/mol
Surface area27490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.22, 92.33, 127.78
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: 39952.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: yydG, BSU40170 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q45595

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Non-polymers , 5 types, 204 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


Type: L-peptide linking / 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.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.81 Å3/Da / Density % sol: 56.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 17.5% (w/v) PEG 1000, 0.1 M 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: Jul 15, 2021 / Details: KB Mirrors
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: 2.4→48.97 Å / Num. obs: 534028 / % possible obs: 99.8 % / Redundancy: 14.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.038 / Rrim(I) all: 0.146 / Net I/σ(I): 12.7
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 1.595 / Num. unique obs: 48252 / CC1/2: 0.724 / Rpim(I) all: 0.46 / Rrim(I) all: 1.661

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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 Exprimental model

Resolution: 2.4→48.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.295 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.302 / SU Rfree Blow DPI: 0.208 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 1801 -RANDOM
Rwork0.1929 ---
obs0.1944 36021 99.8 %-
Displacement parametersBiso mean: 66.65 Å2
Baniso -1Baniso -2Baniso -3
1--6.9309 Å20 Å20 Å2
2--12.3518 Å20 Å2
3----5.4209 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 178 179 5580
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085556HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.917485HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1984SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes935HARMONIC5
X-RAY DIFFRACTIONt_it5556HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion717SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4385SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.98
X-RAY DIFFRACTIONt_other_torsion17.56
LS refinement shellResolution: 2.4→2.42 Å
RfactorNum. reflection% reflection
Rfree0.3735 36 -
Rwork0.3431 --
obs0.3446 721 91.2 %
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)
12.1096-0.4535-0.31161.3279-0.09161.1858-0.0096-0.03790.0745-0.0379-0.05120.07180.07450.07180.0608-0.0713-0.0513-0.0212-0.1524-0.0269-0.1702-1.1688-13.951123.3845
22.32880.02350.78261.6194-0.01791.65430.08960.01710.0210.0171-0.0525-0.06750.021-0.0675-0.0371-0.1062-0.03130.0319-0.14630.0162-0.1439-31.4773-27.341222.7769
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 317
2X-RAY DIFFRACTION1{ A|* }A401 - 507
3X-RAY DIFFRACTION1{ A|* }A601 - 690
4X-RAY DIFFRACTION2{ B|* }B-2 - 317
5X-RAY DIFFRACTION2{ B|* }B401 - 512
6X-RAY DIFFRACTION2{ B|* }B601 - 689

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