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- PDB-7xtg: Cryo-EM structure of Listeria monocytogenes man-PTS complexed wit... -

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Basic information

Entry
Database: PDB / ID: 7xtg
TitleCryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1
Components
  • Bacteriocin curvacin-A
  • Mannose permease IIC component
  • Mannose permease IID component
  • Sakacin-A immunity factor
KeywordsMEMBRANE PROTEIN / Bacteriocin / PTS / ManYZ / ManY / ManZ / transporter / Mannose / PROTEIN TRANSPORT / Listeria monocytogenes / Pediococcus acidilactici / Latilactobacillus sakei / Mannose Phosphotransferase System / Man-PTS
Function / homology
Function and homology information


bacteriocin immunity / phosphoenolpyruvate-dependent sugar phosphotransferase system / killing of cells of another organism / defense response to bacterium / extracellular region / plasma membrane
Similarity search - Function
Bacteriocin-type signal sequence / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Bacteriocin class IIa domain superfamily / Class II bacteriocin / Bacteriocin class IIa family signature. / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component ...Bacteriocin-type signal sequence / Bacteriocin, class IIa / Bacteriocin, class IIa, conserved site / Bacteriocin class IIa domain superfamily / Class II bacteriocin / Bacteriocin class IIa family signature. / Phosphotransferase system, mannose/fructose/sorbose family, IIC subunit / Phosphotransferase system, mannose/fructose/sorbose family IID component / PTS system sorbose-specific iic component / PTS system mannose/fructose/sorbose family IID component / PTS_EIIC type-4 domain profile. / PTS_EIID domain profile. / :
Similarity search - Domain/homology
alpha-D-mannopyranose / Mannose permease IID component / Mannose permease IIC component / Bacteriocin curvacin-A / Sakacin-A immunity factor
Similarity search - Component
Biological speciesPediococcus acidilactici (bacteria)
Latilactobacillus sakei (bacteria)
Listeria monocytogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsZeng, J.W. / Wang, J.W. / Zhu, L.Y.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Appl Environ Microbiol / Year: 2022
Title: Structural Basis of the Immunity Mechanisms of Pediocin-like Bacteriocins.
Authors: Liyan Zhu / Jianwei Zeng / Jiawei Wang /
Abstract: Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic ...Pediocin-like bacteriocins, also designated class IIa bacteriocins, are ribosomally synthesized antimicrobial peptides targeting species closely related to the producers. They act on the cytoplasmic membrane of Gram-positive cells by dissipating the transmembrane electrical potential through pore formation with the mannose phosphotransferase system (man-PTS) as the target/receptor. Bacteriocin-producing strains also synthesize a cognate immunity protein that protects them against their own bacteriocins. Herein, we report the cryo-electron microscopy structure of the bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. The complex structure reveals that pediocin-like bacteriocins bind to the same position on the Core domain of man-PTS, while the C-terminal helical tails of bacteriocins delimit the opening range of the Core domain away from the Vmotif domain to facilitate transmembrane pore formation. Upon attack of bacteriocins from the extracellular side, man-PTS exposes its cytosolic side for recognition of the N-terminal four-helix bundle of the immunity protein. The C-terminal loop of the immunity protein then inserts into the pore and blocks leakage induced by bacteriocins. Elucidation of the toxicity and immunity mechanisms of pediocin-like bacteriocins could support the design of novel bacteriocins against antibiotic-resistant pathogenic bacteria. Pediocin-like bacteriocins, ribosomally synthesized antimicrobial peptides, are generally co-expressed with cognate immunity proteins to protect the bacteriocin-producing strain from its own bacteriocin. Bacteriocins are considered potential alternatives to conventional antibiotics in the context of the bacterial resistance crisis, but the immunity mechanism is unclear. This study uncovered the mechanisms of action and immunity of class IIa bacteriocins.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacteriocin curvacin-A
B: Sakacin-A immunity factor
C: Bacteriocin curvacin-A
D: Mannose permease IIC component
E: Mannose permease IID component
F: Sakacin-A immunity factor
G: Bacteriocin curvacin-A
H: Mannose permease IIC component
I: Mannose permease IID component
J: Sakacin-A immunity factor
Y: Mannose permease IIC component
Z: Mannose permease IID component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,90115
Polymers219,36112
Non-polymers5403
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Bacteriocin curvacin-A


Mass: 4444.088 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus acidilactici (bacteria) / Gene: curA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A311
#2: Protein Sakacin-A immunity factor


Mass: 10213.867 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Latilactobacillus sakei (bacteria) / Gene: saiA / Production host: Escherichia coli (E. coli) / References: UniProt: Q48864
#3: Protein Mannose permease IIC component / Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose/fructose/sorbose ...Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose/fructose/sorbose transporter subunit IIC / Phosphotransferase system (PTS) fructose-specific enzyme IIC component


Mass: 25461.646 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: manY, levF, CW750_06585, GJ664_06230, LAS9624_02106, LSAJ64_0482
Production host: Escherichia coli (E. coli) / References: UniProt: A0A094YUG1
#4: Protein Mannose permease IID component / PTS mannose family transporter subunit IID / Phosphotransferase system (PTS) fructose-specific ...PTS mannose family transporter subunit IID / Phosphotransferase system (PTS) fructose-specific enzyme IID component


Mass: 33000.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: levG, manZ, CW750_06590, GJ664_06235, LAS9624_02107, LSAJ64_0483
Production host: Escherichia coli (E. coli) / References: UniProt: A0A094XZA1
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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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: Cryo-EM structure of Listeria monocytogenes man-PTS complexed with pediocin PA-1 and sakacin-A immunity factor
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Listeria monocytogenes (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 178777 / Symmetry type: POINT

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