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- PDB-9m06: Outer membrane lipoprotein QseG of Salmonella enterica serovar Ty... -

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Basic information

Entry
Database: PDB / ID: 9m06
TitleOuter membrane lipoprotein QseG of Salmonella enterica serovar Typhimurium SL1344
ComponentsOuter membrane lipoprotein
KeywordsSIGNALING PROTEIN / signal activation
Function / homologyQuorum-sensing regulator protein G / YfhG lipoprotein / ACETATE ION / DI(HYDROXYETHYL)ETHER / Hypothetical membrane protein
Function and homology information
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGao, X. / Li, G.B. / Gong, P.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32200144 China
CitationJournal: mBio / Year: 2025
Title: Cryo-EM structure of the QseG-QseE complex reveals an accessory protein-driven two-component system activation mechanism.
Authors: Piqian Gong / Guobang Li / Weixun Li / Mengyuan Xu / Xuyao Jiao / Xudong Chen / Beile Gao / Xiang Gao /
Abstract: The two-component system (TCS) enables bacteria to sense and respond to environmental changes through histidine kinase-mediated signaling cascades. Although the core components of TCSs have been ...The two-component system (TCS) enables bacteria to sense and respond to environmental changes through histidine kinase-mediated signaling cascades. Although the core components of TCSs have been extensively studied, the molecular basis of accessory proteins in modulating histidine kinase activity remains poorly understood. Here, we report that the outer membrane lipoprotein QseG functions as an accessory protein that directly binds to and activates the histidine kinase QseE via its C-terminal domain. Cryo-electron microscopy (Cryo-EM) structural analysis of the QseG-QseE complex reveals a novel yet conserved interaction mode between an accessory lipoprotein and a histidine kinase, which bridges the outer membrane to cytoplasm. Furthermore, systematic truncation assays and photo-crosslinking experiments indicate that outer membrane-anchored QseG is sufficient and prone to engage with and activate the inner membrane histidine kinase QseE under cultured conditions. Our findings provide mechanistic details for accessory lipoprotein-mediated TCS activation, expanding our understanding of bacterial signaling. The evolutionary conservation of this interaction across bacterial pathogens underscores its broad biological significance and potential as a therapeutic target.IMPORTANCEThe classical TCS system in bacterial signal transduction is composed of two proteins-a histidine kinase and its cognate response regulator. More and more studies have revealed the presence of accessory proteins that can modulate the histidine kinase activity and affect signal transduction, but their mechanisms remain largely elusive. This study unveils a previously unrecognized mechanism by which bacterial accessory lipoproteins mediate TCS activation. We provide compelling evidence that QseG directly interacts with QseE through an evolutionarily conserved structural interface, readily and sufficiently activating QseE's autokinase activity and downstream signaling. Given the essential role of QseEF in bacterial virulence and stress adaptation, our findings pave the way for the development of antimicrobial strategies targeting this conserved lipoprotein-mediated activation mechanism.
History
DepositionFeb 24, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer membrane lipoprotein
B: Outer membrane lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8727
Polymers42,5302
Non-polymers3425
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-36 kcal/mol
Surface area15030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 41.001, 126.658
Angle α, β, γ (deg.)90.000, 103.180, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Outer membrane lipoprotein / Two-component system QseEF-associated lipoprotein QseG


Mass: 21265.014 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Gene: yfhG, qseG, SL1344_2525, G1W50_19190, G1W53_19070, G1W54_19660, G1W56_19535, G1W63_19335, G1W64_19365, G1W86_18045, G1W87_18985, G1W89_18830, G1W92_18735, G1X03_18695, G1X04_08460, G1X09_19680, ...Gene: yfhG, qseG, SL1344_2525, G1W50_19190, G1W53_19070, G1W54_19660, G1W56_19535, G1W63_19335, G1W64_19365, G1W86_18045, G1W87_18985, G1W89_18830, G1W92_18735, G1X03_18695, G1X04_08460, G1X09_19680, G1X10_19590, G1X13_19670, G1X17_20470, G1X23_19065, G1X29_19380, G1X32_19630, G1X38_19925, G1X42_18740, G1X47_19355, G1X49_18700, G1X51_19680, G1X52_19370, G1X66_19045, G1X68_16400, G1X69_19950, G1X71_19685, G1X76_19340, G1X80_18180, G1X84_18735, G1X85_19495, G1X86_19670, G1X94_19190, G1X96_19675, G1X99_19370, G1Y02_19370
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3NKH9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 15% (w/v) PEG8000, 0.1 M sodium cacodylate pH 6.7, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 26629 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 0.977 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.18 Å / Num. unique obs: 2506 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→37.14 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 3112 7.7 %
Rwork0.2102 37281 -
obs0.212 25894 77.8 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 23 189 2508
LS refinement shellResolution: 2.1→2.13 Å
RfactorNum. reflection% reflection
Rfree0.3292 60 -
Rwork0.3203 721 -
obs--33 %

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