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- EMDB-50910: Structure of MadB, a class I dehydrates from Clostridium maddingl... -

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Basic information

Entry
Database: EMDB / ID: EMD-50910
TitleStructure of MadB, a class I dehydrates from Clostridium maddingley in the apo state
Map data
Sample
  • Organelle or cellular component: MadB
    • Protein or peptide: Thiopeptide-type bacteriocin biosynthesis domain containing protein
Keywordslanthipeptides / dehydratases / cryo-EM structure / class I lantibiotic / BIOSYNTHETIC PROTEIN
Function / homologyLantibiotic dehydratase, N-terminal / Lantibiotic dehydratase, N terminus / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term / Thiopeptide-type bacteriocin biosynthesis domain containing protein
Function and homology information
Biological speciesClostridium maddingley (bacteria) / Clostridium sp. Maddingley MBC34-26 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKnospe CV / Ortiz J / Reiners J / Kedrov A / Gertzen C / Smits SHJ / Schmitt L
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schm1279/13-1 Germany
German Research Foundation (DFG)417919780 Germany
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into the substrate binding mechanism of the class I dehydratase MadB.
Authors: C Vivien Knospe / Julio Ortiz / Jens Reiners / Alexej Kedrov / Christoph G W Gertzen / Sander H J Smits / Lutz Schmitt /
Abstract: In the battle against antimicrobial resistance, lantibiotics have emerged as promising new sources for antimicrobial drugs. Their exceptional stability is due to characteristic modifications termed ...In the battle against antimicrobial resistance, lantibiotics have emerged as promising new sources for antimicrobial drugs. Their exceptional stability is due to characteristic modifications termed (methyl-)lanthionine rings. Genome mining efforts have identified hundreds of lantibiotics by detecting gene operons, so-called biosynthetic gene clusters (BGC), which encode cysteine-rich peptides (30-50 amino acids in size) and enzymes responsible for dehydration and cyclization, catalyzing the post-translational ring formation. One such identified, class I lantibiotic is maddinglicin from Clostridium maddingley. Here, we present single particle cryo-EM structures of the dehydratase MadB in both, its apo-state and in complex with a leader peptide of maddinglicin, revealing a distinct conformational change upon substrate binding. Small-angle X-ray scattering studies elucidate the substrate binding site for the C-terminal part of maddinglicin. Furthermore, a substrate specificity analysis was performed highlighting a critical stretch of amino acids within the maddinglicin leader sequence that is crucial for binding. Here, we provide molecular insights into the conformational changes, principles of substrate recognition and ligand:protein stoichiometry of a class I lantibiotic dehydratase.
History
DepositionJul 6, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50910.png

Downloads & links

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Map

FileDownload / File: emd_50910.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.004 Å		0.84 Å/pix.
x 360 pix.
= 302.004 Å		0.84 Å/pix.
x 360 pix.
= 302.004 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.1
Minimum - Maximum-4.9958167 - 9.048486
Average (Standard dev.)0.008607632 (±0.2331603)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50910_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_50910_half_map_2.map
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Sample components

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Entire : MadB

EntireName: MadB
Components
  • Organelle or cellular component: MadB
    • Protein or peptide: Thiopeptide-type bacteriocin biosynthesis domain containing protein

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Supramolecule #1: MadB

SupramoleculeName: MadB / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium maddingley (bacteria)
Molecular weightTheoretical: 122.9 kDa/nm

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Macromolecule #1: Thiopeptide-type bacteriocin biosynthesis domain containing protein

MacromoleculeName: Thiopeptide-type bacteriocin biosynthesis domain containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sp. Maddingley MBC34-26 (bacteria)
Molecular weightTheoretical: 123.092266 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRDLYRNTNT FMIRTPIFSI DNYYEFFRKD GESDKIKDRL LEICNNSVFR EAILVSSKSL YSTIIDFCDG KEIKKFDYFL QSIYKYLIR MSMRPTPFGL FSGVDFGKYA EETVISYEND NFKKFARPDL EWIIKIVKEL EDNHYKNLTF KINDSIFIKG E RALLIHST ...String:
MRDLYRNTNT FMIRTPIFSI DNYYEFFRKD GESDKIKDRL LEICNNSVFR EAILVSSKSL YSTIIDFCDG KEIKKFDYFL QSIYKYLIR MSMRPTPFGL FSGVDFGKYA EETVISYEND NFKKFARPDL EWIIKIVKEL EDNHYKNLTF KINDSIFIKG E RALLIHST DKEDNNRIGE ISIRATKPFM RTYDLAKDGI EYNKLKYILI DEYSIEDESK IDNFLKQLIE REFLISNLRP PL TVLDQFD YLINEVKKAE IEIPLVDELT EIKEKLKLYN ETPVGAGEET YLELYKKMES VANVKNILQV DMKLNLRDKK INK KIISDV NDLMNILLDL SMSIENPEPF LSKYKQEFIE KYGQDREISL LEMLDNDIGI GPPMNYERPR NNRSLDVSVN ELLD NNVRD YFMEKYFQAL KTNSRNIAIR DDEIKNLELQ KIDYENIPDS LEINLLVKNK SEDNLSDEFQ YYIGPNLGST SAGKS FGRF SHMMSEPKKF FEELDERNIE LIDSEEYVTC EISYLPSEVR NANVTRNIHS SEYEMSLFTN GSKDNLYRIK LNDIYI GLE NNTFYAKSKT LNKKLLLTIN NMLNPQTAPN AIRFLNDISL DEKKLWYKFV WSDVYKDFSY IPAIKYKNFV IMPETWK MN KINMKINKKT EFNEFKNQFN DYRIKYGVPQ YVYITFADNR ILLNLDDEQC VKILYHECKN SFNEIILNSY EEEGVNIV K ESHKDYICEL VIPLTKIKQE TISDKVSARM LSSDISSLSK ERVKDPFDEW LYIKLYGISS NVDDLIAYYI SEFCNELVE EEIISKYFFM RYVDPEQHIR LRLNSSQEKL LMIYPKIREW LSMIRKKGLM TYFSIDSYDR EIERYGGIEL INIAEKVFFF DSIVTEDIL RAKREGSFDF CDEIIGMISV VHYMESFGLP YAKQVEFLRS QVSSSEYRED FKQKRTEYMK LCNSNKDWEG L RESEEGNI LIEILNKRRK IIEYYGNKVR ENEEVSTDLS ILDSIIHLNC NRMFGIDREF EKKVRALASH ALYALKHFKS

UniProtKB: Thiopeptide-type bacteriocin biosynthesis domain containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsThe sample was mono disperse

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 800314
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9g04:
Structure of MadB, a class I dehydrates from Clostridium maddingley in the apo state

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