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- PDB-6aht: Plasmid partitioning protein TubR from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 6aht
TitlePlasmid partitioning protein TubR from Bacillus cereus
Components(Conserved hypothetical plasmid protein) x 2
KeywordsTRANSCRIPTION / plasmid segregation
Function / homologyConserved hypothetical plasmid protein / Cell division protein FtsZ
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
Model detailscytoskeletal protein
AuthorsHayashi, I.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan
CitationJournal: J Mol Biol / Year: 2018
Title: Cooperative DNA Binding of the Plasmid Partitioning Protein TubR from the Bacillus cereus pXO1 Plasmid.
Authors: Ikuko Hayashi / Takashi Oda / Mamoru Sato / Sotaro Fuchigami /
Abstract: Tubulin/FtsZ-like GTPase TubZ is responsible for maintaining the stability of pXO1-like plasmids in virulent Bacilli. TubZ forms a filament in a GTP-dependent manner, and like other partitioning ...Tubulin/FtsZ-like GTPase TubZ is responsible for maintaining the stability of pXO1-like plasmids in virulent Bacilli. TubZ forms a filament in a GTP-dependent manner, and like other partitioning systems of low-copy-number plasmids, it requires the centromere-binding protein TubR that connects the plasmid to the TubZ filament. Systems regulating TubZ partitioning have been identified in Clostridium prophages as well as virulent Bacillus species, in which TubZ facilitates partitioning by binding and towing the segrosome: the nucleoprotein complex composed of TubR and the centromere. However, the molecular mechanisms of segrosome assembly and the transient on-off interactions between the segrosome and the TubZ filament remain poorly understood. Here, we determined the crystal structure of TubR from Bacillus cereus at 2.0-Å resolution and investigated the DNA-binding ability of TubR using hydroxyl radical footprinting and electrophoretic mobility shift assays. The TubR dimer possesses 2-fold symmetry and binds to a 15-bp palindromic consensus sequence in the tubRZ promoter region. Continuous TubR-binding sites overlap each other, which enables efficient binding of TubR in a cooperative manner. Interestingly, the segrosome adopts an extended DNA-protein filament structure and likely gains conformational flexibility by introducing non-consensus residues into the palindromes in an asymmetric manner. Together, our experimental results and structural model indicate that the unique centromere recognition mechanism of TubR allows transient complex formation between the segrosome and the dynamic polymer of TubZ.
History
DepositionAug 20, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Conserved hypothetical plasmid protein
B: Conserved hypothetical plasmid protein


Theoretical massNumber of molelcules
Total (without water)26,1882
Polymers26,1882
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-19 kcal/mol
Surface area12810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.242, 73.442, 73.729
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 Conserved hypothetical plasmid protein / DNA-binding protein


Mass: 12958.360 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: B4079_0267, B4088_5712, B4155_3158, BACERE00184_00148, BACERE00191_00055, BcAH187_pCER270_0087
Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1BYM8, UniProt: A1BZ87*PLUS
#2: Protein Conserved hypothetical plasmid protein / DNA-binding protein


Mass: 13229.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria)
Gene: B4079_0267, B4088_5712, B4155_3158, BACERE00184_00148, BACERE00191_00055, BcAH187_pCER270_0087
Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1BYM8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 280 K / Method: batch mode / pH: 8 / Details: NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 21, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32509 / % possible obs: 99.6 % / Redundancy: 9.5 % / Net I/σ(I): 22.1
Reflection shellResolution: 2→2.04 Å

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
CNSrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MAD / Resolution: 2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2203 3181 9.5 %
Rwork0.1784 --
obs-32509 97.1 %
Solvent computationBsol: 38.2541 Å2
Displacement parametersBiso max: 87.25 Å2 / Biso mean: 21.398 Å2 / Biso min: 4.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.879 Å20 Å2-0 Å2
2---3.431 Å2-0 Å2
3---1.551 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 0 213 1994
Biso mean---25.73 -
Num. residues----220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2.0151.5
X-RAY DIFFRACTIONc_scbond_it3.152
X-RAY DIFFRACTIONc_mcangle_it2.8482
X-RAY DIFFRACTIONc_scangle_it4.3242.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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