Structure of Prevotella intermedia prointerpain A fragment 39-359 (mutant C154A)

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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A New Autocatalytic Activation Mechanism for Cysteine Proteases Revealed by Prevotella intermedia Interpain A

Mallorqui-Fernandez, N.Manandhar, S.P.Mallorqui-Fernandez, G.Uson, I.Wawrzonek, K.Kantyka, T.Sola, M.Thogersen, I.B.Enghild, J.J.Potempa, J.Gomis-Ruth, F.X.

(2008) J Biol Chem 283: 2871-2882

  • DOI: https://doi.org/10.1074/jbc.M708481200
  • Primary Citation of Related Structures:  
    3BB7, 3BBA

  • PubMed Abstract: 

    Prevotella intermedia is a major periodontopathogen contributing to human gingivitis and periodontitis. Such pathogens release proteases as virulence factors that cause deterrence of host defenses and tissue destruction. A new cysteine protease from the cysteine-histidine-dyad class, interpain A, was studied in its zymogenic and self-processed mature forms. The latter consists of a bivalved moiety made up by two subdomains. In the structure of a catalytic cysteine-to-alanine zymogen variant, the right subdomain interacts with an unusual prodomain, thus contributing to latency. Unlike the catalytic cysteine residue, already in its competent conformation in the zymogen, the catalytic histidine is swung out from its active conformation and trapped in a cage shaped by a backing helix, a zymogenic hairpin, and a latency flap in the zymogen. Dramatic rearrangement of up to 20A of these elements triggered by a tryptophan switch occurs during activation and accounts for a new activation mechanism for proteolytic enzymes. These findings can be extrapolated to related potentially pathogenic cysteine proteases such as Streprococcus pyogenes SpeB and Porphyromonas gingivalis periodontain.

  • Organizational Affiliation

    Departament de Biologia Estructural, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Cientificas, c/Jordi Girona 18-26, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
interpain A321Prevotella intermediaMutation(s): 1 
Gene Names: PIN0048
Find proteins for A9J7N5 (Prevotella intermedia)
Explore A9J7N5 
Go to UniProtKB:  A9J7N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA9J7N5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.87α = 90
b = 38.81β = 127.26
c = 78.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description