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 
  • R-Value Observed: 0.205 

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
  • Structures With Same Primary Citation

  • 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

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Intracellular proteinase inhibitorA120Bacillus subtilisMutation(s): 0 
Gene Names: BSU11130ipiNP_388994.1
Find proteins for P39804 (Bacillus subtilis (strain 168))
Explore P39804 
Go to UniProtKB:  P39804
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

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

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.586α = 90
b = 73.586β = 90
c = 132.923γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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