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- EMDB-34726: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis -

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Basic information

Entry
Database: EMDB / ID: EMD-34726
TitleThe structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
Map data
Sample
  • Complex: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
    • Protein or peptide: Mannose-specific PTS system, IIC component
    • Protein or peptide: Mannose-specific PTS system, IID component
    • Protein or peptide: Lactococcin-A immunity protein
    • Protein or peptide: Bacteriocin lactococcin-A
  • Ligand: alpha-D-mannopyranose
Keywordsantibiotic resistance / antimicrobial peptides / mannose phosphotransferase system / man-PTS / bacteriocins / non-pediocin-like/class IId bacteriocins / lactococcin A / LcnA / immunity / LciA / self-protection / MEMBRANE PROTEIN
Function / homology
Function and homology information


protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-Npi-phosphohistidine-sugar phosphotransferase / bacteriocin immunity / phosphoenolpyruvate-dependent sugar phosphotransferase system / killing of cells of another organism / defense response to bacterium / host cell plasma membrane / extracellular region / membrane / plasma membrane
Similarity search - Function
Bacteriocin, class IId / Lactococcin-A immunity protein-like / Lactococcin-like family / Bacteriocin immunity protein family / 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
Mannose-specific PTS system, IIC component / Mannose-specific PTS system, IID component / Bacteriocin lactococcin-A / Lactococcin-A immunity protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria) / Lactococcus lactis subsp. lactis (lactic acid bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsWang JW
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171190 China
CitationJournal: Appl Environ Microbiol / Year: 2023
Title: Structural Basis of the Mechanisms of Action and Immunity of Lactococcin A, a Class IId Bacteriocin.
Authors: Ruilian Li / Jinsong Duan / Yicheng Zhou / Jiawei Wang /
Abstract: Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for ...Lactococcin A (LcnA), a class IId bacteriocin, induces membrane leakage and cell death by specifically binding to the membrane receptor-mannose phosphotransferase system (man-PTS), as is the case for pediocin-like (class IIa) bacteriocins. The cognate immunity protein of bacteriocins, which protects the producer cell from its own bacteriocin, recognizes and binds to the bacteriocin-man-PTS complex, consequently blocking membrane leakage. We previously deciphered the mode of action and immunity of class IIa bacteriocins. Here, we determined the structure of the ternary complex of LcnA, LciA (, the immunity protein), and its receptor, , the man-PTS of Lactococcus lactis (ll-man-PTS). An external loop on the membrane-located component IIC of ll-man-PTS was found to prevent specific binding of the N-terminal region of LcnA to the site recognized by pediocin-like bacteriocins. Thus, the N-terminal β-sheet region of LcnA recognized an adjacent site on the extracellular side of ll-man-PTS, with the LcnA C-terminal hydrophobic helix penetrating into the membrane. The cytoplasmic cleft formed within the man-PTS Core and Vmotif domains induced by embedded LcnA from the periplasmic side is adopted by the appropriate angle between helices H3 and H4 of the N terminus of LciA. The flexible C terminus of LciA then blocks membrane leakage. To summarize, our findings reveal the molecular mechanisms of action and immunity of LcnA and LciA, laying a foundation for further design of class IId bacteriocins. Class IId (lactococcin-like) bacteriocins and class IIa (pediocin-like) bacteriocins share a few similarities: (i) both induce membrane leakage and cell death by specifically binding the mannose phosphotransferase system (man-PTS) on their target cells, and (ii) cognate immunity proteins recognize and bind to the bacteriocin-man-PTS complex to block membrane leakage. However, class IId bacteriocins lack the "pediocin box" motif, which is typical of class IIa bacteriocins, and basically target only lactococcal cells; in contrast, class IIa bacteriocins target diverse bacterial cells, but not lactococcal cells. We previously solved the structure of class IIa bacteriocin-receptor-immunity ternary complex from Lactobacillus sakei. Here, we determined the structure of the ternary complex of class IId bacteriocin LcnA, its cognate immunity protein LciA, and its receptor, the man-PTS of Lactococcus lactis. By comparing the interactions between man-PTS and class IIa and class IId bacteriocins, this study affords some clues to better understand the specificity of bacteriocins targeting the mannose phosphotransferase system.
History
DepositionNov 12, 2022-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34726.png

Downloads & links

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Map

FileDownload / File: emd_34726.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å		1.07 Å/pix.
x 256 pix.
= 274.995 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0742 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.021
Minimum - Maximum-0.08974916 - 0.16003759
Average (Standard dev.)0.00031073045 (±0.003246254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.9952 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map 1

Fileemd_34726_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_34726_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis

EntireName: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
Components
  • Complex: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
    • Protein or peptide: Mannose-specific PTS system, IIC component
    • Protein or peptide: Mannose-specific PTS system, IID component
    • Protein or peptide: Lactococcin-A immunity protein
    • Protein or peptide: Bacteriocin lactococcin-A
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis

SupramoleculeName: The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria)

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Macromolecule #1: Mannose-specific PTS system, IIC component

MacromoleculeName: Mannose-specific PTS system, IIC component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
EC number: protein-Npi-phosphohistidine-sugar phosphotransferase
Source (natural)Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria)
Molecular weightTheoretical: 27.572371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEYGVLSVIL VIVVAFLAGL EGILDQWQFH QPIIACSLIG IVTGHASAGI ILGGSLQLIA LGWANVGAAV APDAALASIA SSILMVQSN NFDLTHIMGT IVPAAILLAT AGLVLTTLVR MLSVVLVHQA DRAAENGSYS GVEMWHFIAL ICQGLRIAIP A GLLLVISP ...String:
MEYGVLSVIL VIVVAFLAGL EGILDQWQFH QPIIACSLIG IVTGHASAGI ILGGSLQLIA LGWANVGAAV APDAALASIA SSILMVQSN NFDLTHIMGT IVPAAILLAT AGLVLTTLVR MLSVVLVHQA DRAAENGSYS GVEMWHFIAL ICQGLRIAIP A GLLLVISP DAIQKALAAI PPVISGGLAV GGGMVVAVGY AMVINLMATR EVWPFFFLGF ALAPISELTL IATGVLGVVI AI VYLNLQA SGGSGNGTAS SSGDPIGDIL NDY

UniProtKB: Mannose-specific PTS system, IIC component

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Macromolecule #2: Mannose-specific PTS system, IID component

MacromoleculeName: Mannose-specific PTS system, IID component / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
EC number: protein-Npi-phosphohistidine-sugar phosphotransferase
Source (natural)Organism: Lactococcus lactis subsp. lactis (strain KF147) (lactic acid bacteria)
Molecular weightTheoretical: 33.630473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSENKVTLDK KIRRSVMWRS MFLQGSWNYE RMQNGGWAYS LIPALKKLYP SGEEAKEALK RHLEFFNTHP YVAAPIIGVT LALEEERAN GADIDDAAIQ GVKVGMMGPL AGIGDPVFWF TVRPIVGAIA ASLATGGSII APLFFFIVWN AIRIAFLWYT Q EFGYKSGS ...String:
MSENKVTLDK KIRRSVMWRS MFLQGSWNYE RMQNGGWAYS LIPALKKLYP SGEEAKEALK RHLEFFNTHP YVAAPIIGVT LALEEERAN GADIDDAAIQ GVKVGMMGPL AGIGDPVFWF TVRPIVGAIA ASLATGGSII APLFFFIVWN AIRIAFLWYT Q EFGYKSGS AITKDLGGGL LQTVTKGASI LGMFVLGVLI QRWVTINFNG PNAVVSKIPL QKGAYVEFPK GSVSGTQLHD IL GQVGNKL SLDPTKVTYL QDNLNQLIPG LAGLLITLLC MWLLKKKVSP IVIIFGLFVV GILGRWAQIM

UniProtKB: Mannose-specific PTS system, IID component

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Macromolecule #3: Lactococcin-A immunity protein

MacromoleculeName: Lactococcin-A immunity protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria)
Molecular weightTheoretical: 11.179947 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKKKQIEFEN ELRSMLATAL EKDISQEERN ALNIAEKALD NSEYLPKIIL NLRKALTPLA INRTLNHDLS ELYKFITSSK ASNKNLGGG LIMSWGRLF

UniProtKB: Lactococcin-A immunity protein

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Macromolecule #4: Bacteriocin lactococcin-A

MacromoleculeName: Bacteriocin lactococcin-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lactococcus lactis subsp. lactis (lactic acid bacteria)
Molecular weightTheoretical: 5.783341 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KLTFIQSTAA GDLYYNTNTH KYVYQQTQNA FGAAANTIVN GWMGGAAGGF GLHH

UniProtKB: Bacteriocin lactococcin-A

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Macromolecule #5: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 5 / Number of copies: 3 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: EMDB MAP
EMDB ID:

32031

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1529899
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-8hfs:
The structure of LcnA, LciA, and the man-PTS of Lactococcus lactis

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