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- EMDB-50053: Structural basis of specific lysine transport by Pseudomonas aeru... -

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Basic information

Entry
Database: EMDB / ID: EMD-50053
TitleStructural basis of specific lysine transport by Pseudomonas aeruginosa permease LysP
Map data
Sample
  • Complex: PaLysP-NbCA5755 complex
    • Protein or peptide: Lysine-specific permease
    • Protein or peptide: Nanobody CA5755
  • Ligand: LYSINE
KeywordsComplex / MEMBRANE PROTEIN
Function / homologyAmino acid permease, conserved site / : / Amino acid permeases signature. / amino acid transmembrane transport / Amino acid permease/ SLC12A domain / Amino acid permease / amino acid transmembrane transporter activity / membrane / Lysine-specific permease
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsNji E / Matsuoka R
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust222999/Z/21/Z United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of specific lysine transport by Pseudomonas aeruginosa permease LysP.
Authors: Deniz Bicer / Rei Matsuoka / Aurélien F A Moumbock / Preethi Sukumar / Albert Suades / Harish Cheruvara / Andrew Quigley / David Drew / Els Pardon / Jan Steyaert / Peter J F Henderson / ...Authors: Deniz Bicer / Rei Matsuoka / Aurélien F A Moumbock / Preethi Sukumar / Albert Suades / Harish Cheruvara / Andrew Quigley / David Drew / Els Pardon / Jan Steyaert / Peter J F Henderson / Martin Caffrey / Julia J Griese / Emmanuel Nji /
Abstract: Under conditions of extreme acidity, the lysine-specific permease, LysP, not only mediates the import of L-lysine it also interacts with the transcriptional regulator, CadC, to activate expression of ...Under conditions of extreme acidity, the lysine-specific permease, LysP, not only mediates the import of L-lysine it also interacts with the transcriptional regulator, CadC, to activate expression of the cadAB operon. This operon encodes the lysine decarboxylase, CadA, which converts lysine to cadaverine while consuming a cytoplasmic proton, and the antiporter, CadB, which exports protonated cadaverine in exchange for extracellular lysine. Together, these processes contribute to cytoplasmic pH homeostasis and support bacterial acid resistance - a mechanism essential for the survival of pathogenic bacteria in acidic host environments. Here, we present the cryo-EM structure of LysP from Pseudomonas aeruginosa in an inward-occluded conformation (3.2-5.3 Å resolution), bound to L-lysine and a nanobody. L-Lysine is coordinated by hydrophobic contacts, cation-π interactions, and by hydrogen bonding mostly with polar uncharged residues. Reconstitution of LysP into proteoliposomes confirms specific L-lysine transport, which is competitively inhibited by L-4-thialysine. These findings provide a structural framework for understanding selective lysine recognition and inhibition, with implications for antibacterial drug design.
History
DepositionApr 9, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50053.png

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Map

FileDownload / File: emd_50053.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 200 pix.
= 201.6 Å		1.01 Å/pix.
x 200 pix.
= 201.6 Å		1.01 Å/pix.
x 200 pix.
= 201.6 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.008 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.0958
Minimum - Maximum-0.07346717 - 0.29503334
Average (Standard dev.)0.0032354363 (±0.014368322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 201.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50053_msk_1.map
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Additional map: sharpening map

Fileemd_50053_additional_1.map
Annotationsharpening map
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Half map: #2

Fileemd_50053_half_map_1.map
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Half map: #1

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Sample components

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Entire : PaLysP-NbCA5755 complex

EntireName: PaLysP-NbCA5755 complex
Components
  • Complex: PaLysP-NbCA5755 complex
    • Protein or peptide: Lysine-specific permease
    • Protein or peptide: Nanobody CA5755
  • Ligand: LYSINE

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Supramolecule #1: PaLysP-NbCA5755 complex

SupramoleculeName: PaLysP-NbCA5755 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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Macromolecule #1: Lysine-specific permease

MacromoleculeName: Lysine-specific permease / type: protein_or_peptide / ID: 1 / Details: K1001 is a substrate / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)
Molecular weightTheoretical: 51.816453 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: RRVLKPRHLN MIAIGGSIGT GLFVASGATV ATAGPGGALL SYALIGLMVY FLMTSLGEMA AYMPVSGSFC TYGSRFVEDG FGFALGWNY WYNWAVTIAA ELVAAQLVMS FWFPEVPGIY WSAIFLGIMF GLNVISARGF GESEFWFALI KVVTVVIFIG V GLATIFGI ...String:
RRVLKPRHLN MIAIGGSIGT GLFVASGATV ATAGPGGALL SYALIGLMVY FLMTSLGEMA AYMPVSGSFC TYGSRFVEDG FGFALGWNY WYNWAVTIAA ELVAAQLVMS FWFPEVPGIY WSAIFLGIMF GLNVISARGF GESEFWFALI KVVTVVIFIG V GLATIFGI MHGVESPGFS NFTMGDAPFV GGFQAMVGVA MIAGFSFQGT ELIGIAAGES ENPRKNIPIA IRQVFWRILM FY ILAIFVI GMLIPYTDPN LLKNDASDIS VSPFTLLFER AGFAAAAGVM NAVILSAILS AGNSGMYAST RMLYNLALEG KAP RLFSRV SRSGVPRNAL YATTLVGALC FLTSAFGDST VYTWLLNTSG MCGFIAWLGI AISHYRFRKG YLAQGGRLED LPYR AKLFP FGPLFAFALC MVITLGQNYQ ALVGERIDWI GLLATYISLP LFLAIWLGYR WKKRARFVRY HEMDVSPTNT

UniProtKB: Lysine-specific permease

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Macromolecule #2: Nanobody CA5755

MacromoleculeName: Nanobody CA5755 / type: protein_or_peptide / ID: 2 / Details: Nanobody CA5755 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.443981 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
QVQLQESGGG LVQGGSLRLS CAASGRTFSI YGMAWVRQAS GKEREFVAAM PRGGGTTNYA DSVKGRFSIS RDNAKNTVDL QMNSLKPED TAVYYCVADR GFTLRLGIQH DYWGQGTQVT VSSHHHHHHE PEA

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Macromolecule #3: LYSINE

MacromoleculeName: LYSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: LYS
Molecular weightTheoretical: 147.195 Da
Chemical component information

ChemComp-LYS:
LYSINE

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78459
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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