3T91

Structure of the Phosphatase Domain of the Cell Fate Determinant SpoIIE from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the phosphatase domain of the cell fate determinant SpoIIE from Bacillus subtilis.

Levdikov, V.M.Blagova, E.V.Rawlings, A.E.Jameson, K.Tunaley, J.Hart, D.J.Barak, I.Wilkinson, A.J.

(2012) J Mol Biol 415: 343-358

  • DOI: 10.1016/j.jmb.2011.11.017
  • Primary Citation of Related Structures:  
    3T91, 3T9Q

  • PubMed Abstract: 
  • Sporulation in Bacillus subtilis begins with an asymmetric cell division producing two genetically identical cells with different fates. SpoIIE is a membrane protein that localizes to the polar cell division sites where it causes FtsZ to relocate from mid-cell to form polar Z-rings ...

    Sporulation in Bacillus subtilis begins with an asymmetric cell division producing two genetically identical cells with different fates. SpoIIE is a membrane protein that localizes to the polar cell division sites where it causes FtsZ to relocate from mid-cell to form polar Z-rings. Following polar septation, SpoIIE establishes compartment-specific gene expression in the smaller forespore cell by dephosphorylating the anti-sigma factor antagonist SpoIIAA, leading to the release of the RNA polymerase sigma factor σ(F) from an inhibitory complex with the anti-sigma factor SpoIIAB. SpoIIE therefore couples morphological development to differential gene expression. Here, we determined the crystal structure of the phosphatase domain of SpoIIE to 2.6 Å spacing, revealing a domain-swapped dimer. SEC-MALLS (size-exclusion chromatography with multi-angle laser light scattering) analysis however suggested a monomer as the principal form in solution. A model for the monomer was derived from the domain-swapped dimer in which 2 five-stranded β-sheets are packed against one another and flanked by α-helices in an αββα arrangement reminiscent of other PP2C-type phosphatases. A flap region that controls access of substrates to the active site in other PP2C phosphatases is diminished in SpoIIE, and this observation correlates with the presence of a single manganese ion in the active site of SpoIIE in contrast to the two or three metal ions present in other PP2C enzymes. Mapping of a catalogue of mutational data onto the structure shows a clustering of sites whose point mutation interferes with the proper coupling of asymmetric septum formation to sigma factor activation and identifies a surface involved in intramolecular signaling.


    Organizational Affiliation

    Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Stage II sporulation protein EA, B242Bacillus subtilisMutation(s): 0 
Gene Names: BSU00640spoIIEspoIIH
EC: 3.1.3.16
Find proteins for P37475 (Bacillus subtilis (strain 168))
Explore P37475 
Go to UniProtKB:  P37475
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GL0
Query on GL0

Download Ideal Coordinates CCD File 
E [auth B]beta-D-gulopyranose
C6 H12 O6
WQZGKKKJIJFFOK-AIECOIEWSA-N
 Ligand Interaction
MAN
Query on MAN

Download Ideal Coordinates CCD File 
F [auth B]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.618α = 90
b = 87.618β = 90
c = 321.597γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary