2ZTB

Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the parasporin-2 Bacillus thuringiensis toxin that recognizes cancer cells

Akiba, T.Abe, Y.Kitada, S.Kusaka, Y.Ito, A.Ichimatsu, T.Katayama, H.Akao, T.Higuchi, K.Mizuki, E.Ohba, M.Kanai, R.Harata, K.

(2009) J.Mol.Biol. 386: 121-133

  • DOI: 10.1016/j.jmb.2008.12.002

  • PubMed Abstract: 
  • Parasporin-2 is a protein toxin that is isolated from parasporal inclusions of the Gram-positive bacterium Bacillus thuringiensis. Although B. thuringiensis is generally known as a valuable source of insecticidal toxins, parasporin-2 is not insectici ...

    Parasporin-2 is a protein toxin that is isolated from parasporal inclusions of the Gram-positive bacterium Bacillus thuringiensis. Although B. thuringiensis is generally known as a valuable source of insecticidal toxins, parasporin-2 is not insecticidal, but has a strong cytocidal activity in liver and colon cancer cells. The 37-kDa inactive nascent protein is proteolytically cleaved to the 30-kDa active form that loses both the N-terminal and the C-terminal segments. Accumulated cytological and biochemical observations on parasporin-2 imply that the protein is a pore-forming toxin. To confirm the hypothesis, we have determined the crystal structure of its active form at a resolution of 2.38 A. The protein is unusually elongated and mainly comprises long beta-strands aligned with its long axis. It is similar to aerolysin-type beta-pore-forming toxins, which strongly reinforce the pore-forming hypothesis. The molecule can be divided into three domains. Domain 1, comprising a small beta-sheet sandwiched by short alpha-helices, is probably the target-binding module. Two other domains are both beta-sandwiches and thought to be involved in oligomerization and pore formation. Domain 2 has a putative channel-forming beta-hairpin characteristic of aerolysin-type toxins. The surface of the protein has an extensive track of exposed side chains of serine and threonine residues. The track might orient the molecule on the cell membrane when domain 1 binds to the target until oligomerization and pore formation are initiated. The beta-hairpin has such a tight structure that it seems unlikely to reform as postulated in a recent model of pore formation developed for aerolysin-type toxins. A safety lock model is proposed as an inactivation mechanism by the N-terminal inhibitory segment.


    Related Citations: 
    • Crystallization of parasporin-2, a Bacillus thuringiensis crystal protein with selective cytocidal activity against human cells
      Akiba, T.,Abe, Y.,Kitada, S.,Kusaka, Y.,Ito, A.,Ichimatsu, T.,Katayama, H.,Akao, T.,Higuchi, K.,Mizuki, E.,Ohba, M.,Kanai, R.,Harata, K.
      (2004) Acta Crystallogr.,Sect.D 60: 2355
    • A Bacillus thuringiensis crystal protein with selective cytocidal action to human cells
      Ito, A.,Sasaguri, Y.,Kitada, S.,Kusaka, Y.,Kuwano, K.,Masutomi, K.,Mizuki, E.,Akao, T.,Ohba, M.
      (2004) J.Biol.Chem. 279: 21282


    Organizational Affiliation

    Biological Information Research Center, AIST, Tsukuba, Ibaraki 305-8566, Japan. toshi-akiba@aist.go.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Crystal protein
A, B
252Bacillus thuringiensis subsp. dakotaMutation(s): 0 
Find proteins for Q7WZI1 (Bacillus thuringiensis subsp. dakota)
Go to UniProtKB:  Q7WZI1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
LU
Query on LU

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Download CCD File 
A, B
LUTETIUM (III) ION
LU
Lu
PSDMOPINLDTFSZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 136.829α = 90.00
b = 136.829β = 90.00
c = 119.268γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-09-29 
  • Released Date: 2009-01-13 
  • Deposition Author(s): Akiba, T.

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance