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- PDB-9g04: Structure of MadB, a class I dehydrates from Clostridium maddingl... -

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Basic information

Entry
Database: PDB / ID: 9g04
TitleStructure of MadB, a class I dehydrates from Clostridium maddingley in the apo state
ComponentsThiopeptide-type bacteriocin biosynthesis domain containing protein
KeywordsBIOSYNTHETIC PROTEIN / lanthipeptides / dehydratases / cryo-EM structure / class I lantibiotic
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 sp. Maddingley MBC34-26 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKnospe, C.V. / Ortiz, J. / Reiners, J. / Kedrov, A. / Gertzen, C. / Smits, S.H.J. / Schmitt, L.
Funding support Germany, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiopeptide-type bacteriocin biosynthesis domain containing protein
B: Thiopeptide-type bacteriocin biosynthesis domain containing protein


Theoretical massNumber of molelcules
Total (without water)246,1852
Polymers246,1852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 123092.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium sp. Maddingley MBC34-26 (bacteria)
Gene: A370_05566 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K6TUQ9
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: MadB / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 122.9 kDa/nm / Experimental value: NO
Source (natural)Organism: Clostridium maddingley (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 (DE3)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: The sample was mono disperse
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: OTHER / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera3.1model fitting
13PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 800314 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00517406
ELECTRON MICROSCOPYf_angle_d0.77223423
ELECTRON MICROSCOPYf_dihedral_angle_d13.2276736
ELECTRON MICROSCOPYf_chiral_restr0.072540
ELECTRON MICROSCOPYf_plane_restr0.013002

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