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- PDB-7cci: Acinetobacter baumannii response regulator AdeR with disordered N... -

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Basic information

Entry
Database: PDB / ID: 7cci
TitleAcinetobacter baumannii response regulator AdeR with disordered N terminus
ComponentsAdeR
KeywordsDNA BINDING PROTEIN / Acinetobacter Baumannii / Response regulator / AdeR / receiver domain
Function / homology
Function and homology information


phosphorelay response regulator activity / protein-DNA complex / transcription cis-regulatory region binding / regulation of DNA-templated transcription / metal ion binding / cytosol
Similarity search - Function
OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. ...OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Transcriptional regulatory protein WalR-like / Signal transduction response regulator, C-terminal effector / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / Response regulator / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsWen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870132 China
CitationJournal: iScience / Year: 2021
Title: Proteolysis and multimerization regulate signaling along the two-component regulatory system AdeRS.
Authors: Zhenlin Ouyang / Fang Zheng / Li Zhu / Jan Felix / Di Wu / Ke Wu / Irina Gutsche / Yi Wu / Peter M Hwang / Junjun She / Yurong Wen /
Abstract: Bacterial two-component regulatory systems are ubiquitous environment-sensing signal transducers involved in pathogenesis and antibiotic resistance. The two-component regulatory system AdeRS is made ...Bacterial two-component regulatory systems are ubiquitous environment-sensing signal transducers involved in pathogenesis and antibiotic resistance. The two-component regulatory system AdeRS is made up of a sensor histidine kinase AdeS and a cognate response regulator AdeR, which together reduce repression of the multidrug-resistant efflux pump AdeABC. Herein we demonstrate that an N-terminal intrinsically disordered tail in AdeR is important for the upregulation of expression, although it greatly increases the susceptibility of AdeR to proteasome-mediated degradation. We also show that AdeS assembles into a hexameric state that is necessary for its full histidine kinase activity, which appears to occur via autophosphorylation. Taken together, this study demonstrates new structural mechanisms through which two-component systems can transduce environmental signals to impact gene expression and enlightens new potential antimicrobial approach by targeting two-component regulatory systems.
History
DepositionJun 17, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AdeR
B: AdeR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9315
Polymers32,8582
Non-polymers733
Water6,251347
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.885, 70.975, 53.250
Angle α, β, γ (deg.)90.000, 107.065, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein AdeR / Efflux system DNA-binding response regulator AdeR


Mass: 16428.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: adeR, FJV14_17460 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6TA00
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6.0 M Ammonium nitrate, 0.1 M BIS-TRIS propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.65→41.37 Å / Num. obs: 28508 / % possible obs: 95.12 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.87 Å2 / CC1/2: 0.998 / Net I/σ(I): 24.1
Reflection shellResolution: 1.65→1.71 Å / Num. unique obs: 1993 / CC1/2: 0.987

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5J

5x5j


Resolution: 1.65→41.37 Å / SU ML: 0.1513 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 19.0553
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1858 2014 7.07 %
Rwork0.1544 26484 -
obs0.1567 28498 95.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→41.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2119 0 3 347 2469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622193
X-RAY DIFFRACTIONf_angle_d0.81342982
X-RAY DIFFRACTIONf_chiral_restr0.059348
X-RAY DIFFRACTIONf_plane_restr0.0054391
X-RAY DIFFRACTIONf_dihedral_angle_d29.9913298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.235960.1691272X-RAY DIFFRACTION65.02
1.69-1.740.23151170.17881548X-RAY DIFFRACTION77.51
1.74-1.790.20821350.161760X-RAY DIFFRACTION89.98
1.79-1.840.21591500.17461993X-RAY DIFFRACTION99.81
1.84-1.910.23531390.16061986X-RAY DIFFRACTION100
1.91-1.990.19291550.15861973X-RAY DIFFRACTION99.91
1.99-2.080.21441510.15761986X-RAY DIFFRACTION99.72
2.08-2.190.21041580.15471990X-RAY DIFFRACTION100
2.19-2.320.1861470.15211990X-RAY DIFFRACTION99.86
2.32-2.50.19811450.15981978X-RAY DIFFRACTION100
2.5-2.750.17921610.1591980X-RAY DIFFRACTION99.95
2.75-3.150.17821520.15772004X-RAY DIFFRACTION99.95
3.15-3.970.15691570.13671991X-RAY DIFFRACTION99.95
3.97-41.370.16321510.15062033X-RAY DIFFRACTION99.45

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