3ISY

Crystal structure of an intracellular proteinase inhibitor (ipi, bsu11130) from bacillus subtilis at 2.61 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The first structure in a family of peptidase inhibitors reveals an unusual Ig-like fold.

Rigden, D.J.Xu, Q.Chang, Y.Eberhardt, R.Y.Finn, R.D.Rawlings, N.D.

(2013) F1000Res 2: 154-154

  • DOI: 10.12688/f1000research.2-154.v2

  • PubMed Abstract: 
  • We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI) protein from Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a v ...

    We report the crystal structure solution of the Intracellular Protease Inhibitor (IPI) protein from Bacillus subtilis, which has been reported to be an inhibitor of the intracellular subtilisin Isp1 from the same organism. The structure of IPI is a variant of the all-beta, immunoglobulin (Ig) fold. It is possible that IPI is important for protein-protein interactions, of which inhibition of Isp1 is one. The intracellular nature of ISP is questioned, because an alternative ATG codon in the ipi gene would produce a protein with an N-terminal extension containing a signal peptide. It is possible that alternative initiation exists, producing either an intracellular inhibitor or a secreted form that may be associated with the cell surface.  Homologues of the IPI protein from other species are multi-domain proteins, containing signal peptides and domains also associated with the bacterial cell-surface. The cysteine peptidase inhibitors chagasin and amoebiasin also have Ig-like folds, but their topology differs significantly from that of IPI, and they share no recent common ancestor. A model of IPI docked to Isp1 shows similarities to other subtilisin:inhibitor complexes, particularly where the inhibitor interacts with the peptidase active site.


    Organizational Affiliation

    Howard Hughes Medical Institute, Janelia Farm Research Campus, Ashburn VA, 20147, USA.,Joint Center for Structural Genomics, La Jolla CA, 92037, USA ; Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park CA, 94025, USA.,Sandford-Burnham Institute, La Jolla CA, 92037, USA.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK ; European Molecular Biology Laboratory, European Bioinformatics Institute,Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.,Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intracellular proteinase inhibitor
A
120Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: ipi
Find proteins for P39804 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39804
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download SDF File 
Download CCD File 
A
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 73.586α = 90.00
b = 73.586β = 90.00
c = 132.923γ = 90.00
Software Package:
Software NamePurpose
autoSHARPphasing
SHELXphasing
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
SHELXDphasing
REFMACrefinement
MolProbitymodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-06-25
    Type: Database references
  • Version 1.3: 2017-10-25
    Type: Author supporting evidence, Refinement description
  • Version 1.4: 2019-07-24
    Type: Data collection, Derived calculations, Refinement description