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- PDB-8ai2: Crystal structure of radical SAM epimerase EpeE from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 8ai2
TitleCrystal structure of radical SAM epimerase EpeE from Bacillus subtilis with [4Fe-4S] clusters, S-adenosyl-L-homocysteine and RiPP peptide 5 bound
Components
  • Putative exported peptide YydF
  • Putative 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
YydF/SAG 2028 / 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 / Putative exported peptide YydF
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsPolsinelli, I. / Fyfe, C.D. / Legrand, P. / Kubiak, X. / Chavas, L.M.G. / Berteau, O. / Benjdia, A.
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

Downloads & links

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Assembly

Deposited unit
A: Putative peptide biosynthesis protein YydG
B: Putative peptide biosynthesis protein YydG
C: Putative exported peptide YydF
D: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,77837
Polymers82,7504
Non-polymers4,02733
Water3,783210
1
A: Putative peptide biosynthesis protein YydG
C: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,21615
Polymers41,3752
Non-polymers1,84113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-33 kcal/mol
Surface area15090 Å2
MethodPISA
2
B: Putative peptide biosynthesis protein YydG
D: Putative exported peptide YydF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56222
Polymers41,3752
Non-polymers2,18720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-23 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.73, 92.37, 126.72
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 / Protein/peptide , 2 types, 4 molecules ABCD

#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 (bacteria) / References: UniProt: Q45595
#2: Protein/peptide Putative exported peptide YydF


Mass: 1422.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacillus subtilis (bacteria) / References: UniProt: Q45596

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Non-polymers , 5 types, 243 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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
#5: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 14% (w/v) PEG 1000, Tris 0.1 M

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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: 2.39→46.19 Å / Num. obs: 571609 / % possible obs: 99.9 % / Redundancy: 15.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.031 / Rrim(I) all: 0.122 / Net I/σ(I): 14.8
Reflection shellResolution: 2.39→2.48 Å / Rmerge(I) obs: 1.411 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 60066 / CC1/2: 0.84 / Rpim(I) all: 0.366 / Rrim(I) all: 1.458

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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: 2.393→46.19 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.293 / SU Rfree Blow DPI: 0.209 / SU Rfree Cruickshank DPI: 0.209
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1881 -RANDOM
Rwork0.1861 ---
obs0.1879 37607 99.9 %-
Displacement parametersBiso mean: 63.94 Å2
Baniso -1Baniso -2Baniso -3
1--10.168 Å20 Å20 Å2
2--7.7799 Å20 Å2
3---2.3881 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å
Refinement stepCycle: LAST / Resolution: 2.393→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5381 0 204 210 5795
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085775HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.937769HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2056SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes969HARMONIC5
X-RAY DIFFRACTIONt_it5775HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion737SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies8HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact4667SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion17.56
LS refinement shellResolution: 2.393→2.41 Å
RfactorNum. reflection% reflection
Rfree0.3629 38 -
Rwork0.2877 --
obs--96.55 %
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)
11.94710.4328-0.31841.3923-0.00810.97130.0040.07330.00930.0733-0.0506-0.01160.0093-0.01160.04660.00010.0498-0.0085-0.19880.0242-0.19821.0931-14.391-23.2257
22.24030.08210.96121.8460.05492.24220.0674-0.0255-0.0213-0.0255-0.03970.1451-0.02130.1451-0.0277-0.08690.03240.0547-0.2317-0.0091-0.198331.6043-28.0361-22.728
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 317
2X-RAY DIFFRACTION1{ A|* }A401 - 510
3X-RAY DIFFRACTION1{ A|* }A601 - 717
4X-RAY DIFFRACTION2{ B|* }B-5 - 317
5X-RAY DIFFRACTION2{ B|* }B401 - 517
6X-RAY DIFFRACTION2{ B|* }B601 - 693

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