The LIPY/F-motif in an intracellular subtilisin protease is involved in inhibition

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 

Starting Model: experimental
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Mutational analysis of the pro-peptide of a marine intracellular subtilisin protease supports its role in inhibition.

Bjerga, G.E.K.Larsen, O.Williamson, A.Garcia-Moyano, A.Leiros, I.Puntervoll, P.

(2018) Proteins 86: 965-977

  • DOI: https://doi.org/10.1002/prot.25528
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Intracellular subtilisin proteases (ISPs) have important roles in protein processing during the stationary phase in bacteria. Their unregulated protein degrading activity may have adverse effects inside a cell, but little is known about their regulatory mechanism. Until now, ISPs have mostly been described from Bacillus species, with structural data from a single homolog. Here, we study a marine ISP originating from a phylogenetically distinct genus, Planococcus sp. The enzyme was successfully overexpressed in E. coli, and is active in presence of calcium, which is thought to have a role in minor, but essential, structural rearrangements needed for catalytic activity. The ISP operates at alkaline pH and at moderate temperatures, and has a corresponding melting temperature around 60 °C. The high-resolution 3-dimensional structure reported here, represents an ISP with an intact catalytic triad albeit in a configuration with an inhibitory pro-peptide bound. The pro-peptide is removed in other homologs, but the removal of the pro-peptide from the Planococcus sp. AW02J18 ISP appears to be different, and possibly involves several steps. A first processing step is described here as the removal of 2 immediate N-terminal residues. Furthermore, the pro-peptide contains a conserved LIPY/F-motif, which was found to be involved in inhibition of the catalytic activity.

  • Organizational Affiliation

    Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine protease
A, B
330Planococcus plakortidisMutation(s): 0 
Gene Names: BBI15_13285
Find proteins for A0A3B6UEW8 (Planococcus plakortidis)
Explore A0A3B6UEW8 
Go to UniProtKB:  A0A3B6UEW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3B6UEW8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.130 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.17α = 90
b = 85.18β = 90
c = 104.58γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Council of NorwayNorway221568

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-24
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description