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- PDB-9hh1: LysR Type Transcriptional Regulator LsrB from Agrobacterium tumef... -

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Basic information

Entry
Database: PDB / ID: 9hh1
TitleLysR Type Transcriptional Regulator LsrB from Agrobacterium tumefaciens
ComponentsTranscriptional regulator, LysR family
KeywordsDNA BINDING PROTEIN / LysR-type trancriptional regulator / DNA-Binding / Agrobacterium / transcription factor
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesAgrobacterium fabrum str. C58 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsElders, H. / Schmidt, J.J. / Fiedler, R. / Hofmann, E. / Narberhaus, F.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)NA 240/11-2 Germany
German Research Foundation (DFG)Research Training Group 2341 Germany
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Two redox-responsive LysR-type transcription factors control the oxidative stress response of Agrobacterium tumefaciens.
Authors: Janka J Schmidt / Vivian B Brandenburg / Hannah Elders / Saba Shahzad / Sina Schäkermann / Ronja Fiedler / Lisa R Knoke / Yvonne Pfänder / Pascal Dietze / Hannah Bille / Bela Gärtner / ...Authors: Janka J Schmidt / Vivian B Brandenburg / Hannah Elders / Saba Shahzad / Sina Schäkermann / Ronja Fiedler / Lisa R Knoke / Yvonne Pfänder / Pascal Dietze / Hannah Bille / Bela Gärtner / Lennart J Albin / Lars I Leichert / Julia E Bandow / Eckhard Hofmann / Franz Narberhaus /
Abstract: Pathogenic bacteria often encounter fluctuating reactive oxygen species (ROS) levels, particularly during host infection, necessitating robust redox-sensing mechanisms for survival. The LysR-type ...Pathogenic bacteria often encounter fluctuating reactive oxygen species (ROS) levels, particularly during host infection, necessitating robust redox-sensing mechanisms for survival. The LysR-type transcriptional regulator (LTTR) OxyR is a widely conserved bacterial thiol-based redox sensor. However, members of the Rhizobiales also encode LsrB, a second LTTR with potential redox-sensing function. This study explores the roles of OxyR and LsrB in the plant-pathogen Agrobacterium tumefaciens. Through single and combined deletions, we observed increased H2O2 sensitivity, underscoring their function in oxidative defense. Genome-wide transcriptome profiling under H2O2 exposure revealed that OxyR and LsrB co-regulate key antioxidant genes, including katG, encoding a bifunctional catalase/peroxidase. Agrobacterium tumefaciens LsrB possesses four cysteine residues potentially involved in redox sensing. To elucidate the structural basis for redox-sensing, we applied single-particle cryo-EM (cryogenic electron microscopy) to experimentally confirm an AlphaFold model of LsrB, identifying two proximal cysteine pairs. In vitro thiol-trapping coupled with mass spectrometry confirmed reversible thiol modifications of all four residues, suggesting a functional role in redox regulation. Collectively, these findings reveal that A. tumefaciens employs two cysteine-based redox sensing transcription factors, OxyR and LsrB, to withstand oxidative stress encountered in host and soil environments.
History
DepositionNov 20, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LysR family
B: Transcriptional regulator, LysR family


Theoretical massNumber of molelcules
Total (without water)70,7492
Polymers70,7492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Transcriptional regulator, LysR family


Mass: 35374.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium fabrum str. C58 (bacteria)
Gene: Atu2186 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9CI74
Has protein modificationN

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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: Dimeric LTTR-type transcriptional regulator LsrB / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.076 MDa / Experimental value: YES
Source (natural)Organism: Agrobacterium tumefaciens (bacteria)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria)
Buffer solutionpH: 8
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: homogeneous dimeric sample
Specimen supportDetails: 15mA / Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)
EM imaging opticsEnergyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5.3particle selection
7UCSF ChimeraX1.8model fitting
9cryoSPARC4.5.3initial Euler assignment
10cryoSPARC4.5.3final Euler assignment
11cryoSPARC4.5.3classification
12cryoSPARC4.5.33D reconstruction
13UCSF ChimeraX1.8model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 8864865
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 484971 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model

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