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- PDB-7vlx: Cryo-EM structures of Listeria monocytogenes man-PTS -

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Basic information

Entry
Database: PDB / ID: 7vlx
TitleCryo-EM structures of Listeria monocytogenes man-PTS
Components
  • Mannose/fructose/sorbose family PTS transporter subunit IIC
  • PTS mannose family transporter subunit IID
KeywordsMEMBRANE PROTEIN / antimicrobial peptides / bacteriocins / pediocin PA-1 / pediocin-like/class IIa bacteriocins / antibiotic resistance / mannose phosphotransferase / man-PTS
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane / plasma membrane
Similarity search - Function
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 / PTS mannose family transporter subunit IID / Mannose/fructose/sorbose family PTS transporter subunit IIC
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsWang, J.W.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
Ministry of Science and Technology (MoST, China)2016YFA0501103 China
CitationJournal: Appl Environ Microbiol / Year: 2022
Title: Structural Basis of Pore Formation in the Mannose Phosphotransferase System by Pediocin PA-1.
Authors: Liyan Zhu / Jianwei Zeng / Chang Wang / Jiawei Wang /
Abstract: Bacteriocins are ribosomally synthesized bacterial antimicrobial peptides that have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like (or ...Bacteriocins are ribosomally synthesized bacterial antimicrobial peptides that have a narrow spectrum of antibacterial activity against species closely related to the producers. Pediocin-like (or class IIa) bacteriocins (PLBs) exhibit antibacterial activity against several Gram-positive bacterial strains by forming pores in the cytoplasmic membrane of target cells with a specific receptor, the mannose phosphotransferase system (man-PTS). In this study, we report the cryo-electron microscopy structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1, the first and most extensively studied representative PLB, at resolutions of 3.12 and 2.45 Å, respectively. The structures revealed that the binding of pediocin PA-1 opens the Core domain of man-PTS away from its Vmotif domain, creating a pore through the cytoplasmic membranes of target cells. During this process, the N-terminal β-sheet region of pediocin PA-1 can specifically attach to the extracellular surface of the man-PTS Core domain, whereas the C-terminal half penetrates the membrane and cracks the man-PTS like a wedge. Thus, our findings shed light on a design of novel PLBs that can kill the target pathogenic bacteria. Listeria monocytogenes is a ubiquitous microorganism responsible for listeriosis, a rare but severe disease in humans, who become infected by ingesting contaminated food products (i.e., dairy, meat, fish, and vegetables): the disease has a fatality rate of 33%. Pediocin PA-1 is an important commercial additive used in food production to inhibit species. The mannose phosphotransferase system (man-PTS) is responsible for the sensitivity of Listeria monocytogenes to pediocin PA-1. In this study, we report the cryo-EM structures of man-PTS from Listeria monocytogenes alone and its complex with pediocin PA-1 at resolutions of 3.12 and 2.45 Å, respectively. Our results facilitate the understanding of the mode of action of class IIa bacteriocins as an alternative to antibiotics.
History
DepositionOct 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 15, 2021Group: Database references / Category: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
Y: Mannose/fructose/sorbose family PTS transporter subunit IIC
Z: PTS mannose family transporter subunit IID
A: Mannose/fructose/sorbose family PTS transporter subunit IIC
B: PTS mannose family transporter subunit IID
C: Mannose/fructose/sorbose family PTS transporter subunit IIC
D: PTS mannose family transporter subunit IID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,8809
Polymers182,3396
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 Mannose/fructose/sorbose family PTS transporter subunit IIC / PTS mannose/fructose/sorbose transporter subunit IIC / PTS system mannose-specific transporter subunit IIC


Mass: 27377.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: A7N75_11070, A8L61_14515, A8N58_12480, A9809_10565, AB938_12885, ACY06_13095, AF066_07245, AF314_13905, AFT97_02015, AMC55_01930, APE37_07920, ARJ20_12560, ARS65_09750, ART25_13030, B1821_ ...Gene: A7N75_11070, A8L61_14515, A8N58_12480, A9809_10565, AB938_12885, ACY06_13095, AF066_07245, AF314_13905, AFT97_02015, AMC55_01930, APE37_07920, ARJ20_12560, ARS65_09750, ART25_13030, B1821_09270, B1N06_07640, B1N45_09425, B1N52_06240, B1N70_07565, B1O25_12365, B2H17_07955, B4960_11450, B4P04_12550, B4P23_04745, B4X79_07140, B4X80_09510, B4X87_09590, B4X92_08295, B4Y29_05710, B4Y36_09590, B4Y40_06900, B4Y49_08220, B4Y57_09590, B5K59_14490, BBW72_13535, BLH28_04840, C6R69_10580, C7H49_10125, D4920_07280, D9T24_08210, DCT16_05775, DU018_08255, E3W32_13300, E5F58_14000, E5H26_12030, EDX87_01965, EK719_12800, EPI21_11885, EXZ73_03360, F4W64_09720, F6515_08315, FA835_09550, FDP75_01900, FL871_04025, FLQ84_02200, FLQ91_10935, FLQ96_08830, FLR03_08660, FZX01_09955, G3O21_000383, GEH47_13560, GEJ92_13635, GEK33_09035, GER99_09730, GF172_05545, GGA51_12050, GHD27_05540, GIH49_05190, GIQ23_05220, GJA60_00910, GJB11_12355, GJW51_04690, GUM51_00345, GYS09_07230, GYS13_03425, GYS23_07920, GYU49_14700, GYZ23_07710, GYZ34_05285, GZI09_02550, GZI83_01895, GZP37_07990, GZS65_10905, HOY96_00900, HRK24_07015, HXD42_11005, HXF15_12125, KW30_01930, LH97_05170, LmNIHS28_00099, QU69_12075
Production host: Escherichia coli (E. coli) / References: UniProt: S5LAD9
#2: Protein PTS mannose family transporter subunit IID / PTS mannose/fructose/sorbose transporter family subunit IID


Mass: 33402.164 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria)
Gene: ARV28_12335, B4960_11455, CX098_00810, E3W32_13305, E5H26_12035, EDX87_01970, EK719_12795, EYY39_04480, F4W64_09725, FL871_04030, FZX01_09960, GEK33_09040, GH165_06065, GIH49_05195, HRK24_07020
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1E8EBU8
#3: 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

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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: mannose-specific PTS system from Listeria monocytogenes
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Listeria monocytogenes (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: LAB6 / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136729 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312555
ELECTRON MICROSCOPYf_angle_d0.64517079
ELECTRON MICROSCOPYf_dihedral_angle_d4.7871731
ELECTRON MICROSCOPYf_chiral_restr0.0412067
ELECTRON MICROSCOPYf_plane_restr0.0052097

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