Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 35.06 kDa 
• Atom Count: 2823 
• Modelled Residue Count: 314 
• Deposited Residue Count: 321 
• Unique protein chains: 1

3BB7

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

• PDB DOI: 10.2210/pdb3BB7/pdb

• Classification: HYDROLASE
• Organism(s): Prevotella intermedia
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-11-09 Released: 2007-11-20 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.193 
• R-Value Work: 0.155 
• R-Value Observed: 0.156 

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 Biol Chem 283: 2871-2882

• PubMed: 17993455 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
interpain A	A	321	Prevotella intermedia	Mutation(s): 1  Gene Names: pin0048
UniProt
Find proteins for A9J7N5 (Prevotella intermedia) Explore A9J7N5  Go to UniProtKB:  A9J7N5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 128.87	α = 90
b = 38.81	β = 127.26
c = 78.14	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-11-09 
• Released Date: 2007-11-20 
Deposition Author(s): 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.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance