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- PDB-7yhj: Effector binding domain of LysR-Type transcription factor LrhA fr... -

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Basic information

Entry
Database: PDB / ID: 7yhj
TitleEffector binding domain of LysR-Type transcription factor LrhA from E. coli
ComponentsProbable HTH-type transcriptional regulator LrhA
KeywordsTRANSCRIPTION / Transcriptional regulator
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of 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
DI(HYDROXYETHYL)ETHER / Probable HTH-type transcriptional regulator LrhA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.237 Å
AuthorsXie, C. / Jiang, X.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
CitationJournal: J Mol Biol / Year: 2026
Title: Oligomerization-Dependent Regulation of LrhA Controls Bacterial Flagellar Biosynthesis.
Authors: Baichun Niu / Masahide Kikkawa / Xuguang Jiang /
Abstract: LysR-type transcriptional regulators (LTTRs) are a diverse family of proteins that regulate various cellular processes, including motility in bacteria. In Escherichia coli, the LTTR LrhA represses ...LysR-type transcriptional regulators (LTTRs) are a diverse family of proteins that regulate various cellular processes, including motility in bacteria. In Escherichia coli, the LTTR LrhA represses flagellar biosynthesis by inhibiting the flhDC operon. However, the structural basis underlying this regulation has remained unclear. Here, we determined both a high-resolution crystal structure and a cryo-EM reconstruction of LrhA, revealing a predominant and stable tetrameric organization with pronounced structural variability in its effector-binding region. Structural and biochemical analyses demonstrate that mutations in these variable regions perturb the oligomeric equilibrium of LrhA, shifting the balance between tetrameric and dimeric species. This shift correlates with enhanced DNA binding affinity and stronger repression of the flhDC promoter. While ligand binding may similarly modulate LrhA activity, our data primarily support a model in which alterations in oligomeric state mediated by the variable regions regulate LrhA function. Together, these findings provide a structural framework for understanding how LrhA controls bacterial motility and offer broader insights into oligomerization-based regulation within the LTTR family.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Mar 11, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable HTH-type transcriptional regulator LrhA
B: Probable HTH-type transcriptional regulator LrhA
C: Probable HTH-type transcriptional regulator LrhA
D: Probable HTH-type transcriptional regulator LrhA
E: Probable HTH-type transcriptional regulator LrhA
F: Probable HTH-type transcriptional regulator LrhA
G: Probable HTH-type transcriptional regulator LrhA
H: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,99311
Polymers284,6948
Non-polymers2983
Water39622
1
A: Probable HTH-type transcriptional regulator LrhA
C: Probable HTH-type transcriptional regulator LrhA
E: Probable HTH-type transcriptional regulator LrhA
G: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,5496
Polymers142,3474
Non-polymers2022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-47 kcal/mol
Surface area31390 Å2
MethodPISA
2
B: Probable HTH-type transcriptional regulator LrhA
H: Probable HTH-type transcriptional regulator LrhA

D: Probable HTH-type transcriptional regulator LrhA
F: Probable HTH-type transcriptional regulator LrhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,4435
Polymers142,3474
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x+1/2,-y,z-1/21
Buried area6830 Å2
ΔGint-53 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.682, 169.312, 190.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable HTH-type transcriptional regulator LrhA


Mass: 35586.805 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: lrhA, genR, b2289, JW2284 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P36771
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#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.: 22 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.4 Å3/Da / Density % sol: 48.81 % / Description: plate crystal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, 0.1 M HEPES, 0.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.23→50 Å / Num. obs: 43674 / % possible obs: 98.5 % / Redundancy: 5.1 % / CC1/2: 0.977 / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.172 / Rrim(I) all: 0.462 / Net I/σ(I): 3.2
Reflection shellResolution: 3.23→3.35 Å / Redundancy: 5.3 % / Rmerge(I) obs: 1.385 / Num. unique obs: 4278 / CC1/2: 0.5 / Rpim(I) all: 0.89 / Rrim(I) all: 2.385 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONM

3onm


Resolution: 3.237→48.713 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3376 2148 4.94 %RANDOM
Rwork0.3208 41343 --
obs0.3217 43491 97.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.45 Å2 / Biso mean: 36.6604 Å2 / Biso min: 12.75 Å2
Refinement stepCycle: final / Resolution: 3.237→48.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11809 0 17 22 11848
Biso mean--52.27 30 -
Num. residues----1532
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.237-3.3120.40051460.3466240788
3.312-3.39480.32881410.3449270896
3.3948-3.48660.35421380.3435269698
3.4866-3.58910.371150.3341276298
3.5891-3.70490.38581400.3265272298
3.7049-3.83730.33661660.3108272098
3.8373-3.99090.34131450.3091274698
3.9909-4.17240.31441270.3109275298
4.1724-4.39220.33421440.2964276298
4.3922-4.66720.31421550.3009275798
4.6672-5.02720.31421490.3278098
5.0272-5.53250.33311240.3128283299
5.5325-6.33160.3271640.3164281099
6.3316-7.97150.35311560.3268287399
7.9715-48.7130.32631380.3502301699

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