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- PDB-9m07: Histidine kinase QseE sensor domain of Salmonella Typhimurium SL1344 -

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Basic information

Entry
Database: PDB / ID: 9m07
TitleHistidine kinase QseE sensor domain of Salmonella Typhimurium SL1344
Componentshistidine kinase
KeywordsSIGNALING PROTEIN / Histidine kinase
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / phosphorelay response regulator activity / phosphorelay sensor kinase activity / histidine kinase / protein kinase activator activity / ATP binding / plasma membrane
Similarity search - Function
: / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase ...: / Histidine kinase/HSP90-like ATPase / His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / Signal transduction histidine kinase-related protein, C-terminal / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Histidine kinase domain / Histidine kinase domain profile. / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: histidine kinase


Theoretical massNumber of molelcules
Total (without water)14,9851
Polymers14,9851
Non-polymers00
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.452, 55.452, 86.115
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-203-

HOH

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Components

#1: Protein histidine kinase


Mass: 14984.701 Da / Num. of mol.: 1 / Fragment: QseE sensor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 (bacteria)
Gene: G1W55_21660, G1W57_21075, G1W59_09275, G1W66_20535, G1W69_20505, G1W71_21505, G1W72_11380, G1W73_10360, G1W74_21080, G1W84_13470, G1W85_13465, G1W99_23435, G1X00_13645, G1X06_20175, G1X11_ ...Gene: G1W55_21660, G1W57_21075, G1W59_09275, G1W66_20535, G1W69_20505, G1W71_21505, G1W72_11380, G1W73_10360, G1W74_21080, G1W84_13470, G1W85_13465, G1W99_23435, G1X00_13645, G1X06_20175, G1X11_11700, G1X12_12075, G1X15_13125, G1X18_13650, G1X19_12300, G1X27_11005, G1X31_13200, G1X35_19325, G1X41_12250, G1X46_12430, G1X54_21230, G1X75_21695, G1X77_21670, G1X98_13465
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A719LJQ8, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 2.21 Å3/Da / Density % sol: 44.32 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 3.5 M Sodium formate, 0.1 M Tris-HCl pH 8.5

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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: Jun 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 5687 / % possible obs: 99.9 % / Redundancy: 23.5 % / Biso Wilson estimate: 33.12 Å2 / CC1/2: 0.992 / Net I/σ(I): 30
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 541 / CC1/2: 0.985

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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: 2.4→25.49 Å / SU ML: 0.303 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.6454
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2747 537 10.02 %
Rwork0.2226 4823 -
obs0.2279 5360 94.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.98 Å2
Refinement stepCycle: LAST / Resolution: 2.4→25.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 0 31 877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033854
X-RAY DIFFRACTIONf_angle_d0.58281151
X-RAY DIFFRACTIONf_chiral_restr0.0333131
X-RAY DIFFRACTIONf_plane_restr0.0062152
X-RAY DIFFRACTIONf_dihedral_angle_d3.7467122
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.640.33341080.2652987X-RAY DIFFRACTION79.69
2.64-3.020.32551380.25641233X-RAY DIFFRACTION99.49
3.02-3.810.24741400.22131250X-RAY DIFFRACTION99.64
3.81-25.490.25981510.20141353X-RAY DIFFRACTION99.67

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