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- EMDB-50911: Structure of MadB, a class I dehydrates from Clostridium maddingl... -

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Basic information

Entry
Database: EMDB / ID: EMD-50911
TitleStructure of MadB, a class I dehydrates from Clostridium maddingley, in complex with its substrate
Map data
Sample
  • Complex: Binary complex of MadB and MadA
    • Protein or peptide: Thiopeptide-type bacteriocin biosynthesis domain containing protein
    • Protein or peptide: Lantibiotic, gallidermin/nisin family
Keywordslanthipeptides / dehydratases / cryo-EM structure / class I lantibiotic / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region
Similarity search - Function
Lantibiotic, Type A, Bacillales-type / Gallidermin / Lantibiotic dehydratase, N-terminal / Lantibiotic dehydratase, N terminus / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term
Similarity search - Domain/homology
Lantibiotic, gallidermin/nisin family / Thiopeptide-type bacteriocin biosynthesis domain containing protein
Similarity search - Component
Biological speciesClostridium sp. Maddingley MBC34-26 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsKnospe CV / Ortiz J / Reiners J / Kedrov A / Gerten 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 7, 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_50911.png

Downloads & links

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Map

FileDownload / File: emd_50911.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8389 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-8.273004 - 12.610765000000001
Average (Standard dev.)0.0023958774 (±0.26161677)
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_50911_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50911_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Binary complex of MadB and MadA

EntireName: Binary complex of MadB and MadA
Components
  • Complex: Binary complex of MadB and MadA
    • Protein or peptide: Thiopeptide-type bacteriocin biosynthesis domain containing protein
    • Protein or peptide: Lantibiotic, gallidermin/nisin family

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Supramolecule #1: Binary complex of MadB and MadA

SupramoleculeName: Binary complex of MadB and MadA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridium sp. Maddingley MBC34-26 (bacteria)

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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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Macromolecule #2: Lantibiotic, gallidermin/nisin family

MacromoleculeName: Lantibiotic, gallidermin/nisin family / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Clostridium sp. Maddingley MBC34-26 (bacteria)
Molecular weightTheoretical: 5.879029 KDa
SequenceString:
MGKLDDFDLD VKVKADTTKV GPAITSKSLC TPGCITGVLM CITQNSCVSC KSCIKC

UniProtKB: Lantibiotic, gallidermin/nisin family

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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

BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 1.01 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / 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

Particle selectionNumber selected: 2971174
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 994872
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: OTHER

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