3BBA | pdb_00003bba

Structure of active wild-type Prevotella intermedia interpain A cysteine protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 
    0.261 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

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 Biological Chem 283: 2871-2882

  • DOI: https://doi.org/10.1074/jbc.M708481200
  • Primary Citation 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.

Macromolecule Content 

  • Total Structure Weight: 54.7 kDa 
  • Atom Count: 3,797 
  • Modeled Residue Count: 496 
  • Deposited Residue Count: 502 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
interpain A
A, B
251Prevotella intermediaMutation(s): 0 
Gene Names: PIN0048
UniProt
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
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free:  0.261 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.241α = 90
b = 129.241β = 90
c = 81.97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

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: Advisory, Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description