4EI7

Crystal structure of Bacillus cereus TubZ, GDP-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 

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This is version 1.2 of the entry. See complete history


Literature

Filament formation of the FtsZ/tubulin-like protein TubZ from the Bacillus cereus pXO1 plasmid.

Hoshino, S.Hayashi, I.

(2012) J Biol Chem 287: 32103-32112

  • DOI: 10.1074/jbc.M112.373803
  • Primary Citation of Related Structures:  
    4EI7, 4EI8, 4EI9

  • PubMed Abstract: 
  • Stable maintenance of low-copy-number plasmids requires partition (par) systems that consist of a nucleotide hydrolase, a DNA-binding protein, and a cis-acting DNA-binding site. The FtsZ/tubulin-like GTPase TubZ was identified as a partitioning factor of the virulence plasmids pBtoxis and pXO1 in Bacillus thuringiensis and Bacillus anthracis, respectively ...

    Stable maintenance of low-copy-number plasmids requires partition (par) systems that consist of a nucleotide hydrolase, a DNA-binding protein, and a cis-acting DNA-binding site. The FtsZ/tubulin-like GTPase TubZ was identified as a partitioning factor of the virulence plasmids pBtoxis and pXO1 in Bacillus thuringiensis and Bacillus anthracis, respectively. TubZ exhibits high GTPase activity and assembles into polymers both in vivo and in vitro, and its "treadmilling" movement is required for plasmid stability in the cell. To investigate the molecular mechanism of pXO1 plasmid segregation by TubZ filaments, we determined the crystal structures of Bacillus cereus TubZ in apo-, GDP-, and guanosine 5'-3-O-(thio)triphosphate (GTPγS)-bound forms at resolutions of 2.1, 1.9, and 3.3 Å, respectively. Interestingly, the slowly hydrolyzable GTP analog GTPγS was hydrolyzed to GDP in the crystal. In the post-GTP hydrolysis state, GDP-bound B. cereus TubZ forms a dimer by the head-to-tail association of individual subunits in the asymmetric unit, which is similar to the protofilament formation of FtsZ and B. thuringiensis TubZ. However, the M loop interacts with the nucleotide-binding site of the adjacent subunit and stabilizes the filament structure in a different manner, which indicates that the molecular assembly of the TubZ-related par systems is not stringently conserved. Furthermore, we show that the C-terminal tail of TubZ is required for association with the DNA-binding protein TubR. Using a combination of crystallography, site-directed mutagenesis, and biochemical analysis, our results provide the structural basis of the TubZ polymer that may drive DNA segregation.


    Organizational Affiliation

    Department of Supramolecular Biology, Graduate School of Nanobioscience, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasmid replication protein RepXA, B389Bacillus cereus ATCC 10987Mutation(s): 0 
Gene Names: repXBCE_A0070tubZ
EC: 3.6.5
UniProt
Find proteins for Q74P24 (Bacillus cereus (strain ATCC 10987 / NRS 248))
Explore Q74P24 
Go to UniProtKB:  Q74P24
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ74P24
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.826α = 90
b = 76.015β = 104.59
c = 96.931γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-15
    Type: Initial release
  • Version 1.1: 2014-07-23
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description