1YVB

the Plasmodium falciparum Cysteine Protease Falcipain-2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for unique mechanisms of folding and hemoglobin binding by a malarial protease.

Wang, S.X., Pandey, K.C., Somoza, J.R., Sijwali, P.S., Kortemme, T., Brinen, L.S., Fletterick, R.J., Rosenthal, P.J., McKerrow, J.H.

(2006) Proc.Natl.Acad.Sci.Usa 103: 11503-11508

  • DOI: 10.1073/pnas.0600489103

  • PubMed Abstract: 

    • Falcipain-2 (FP2), the major cysteine protease of the human malaria parasite Plasmodium falciparum, is a hemoglobinase and promising drug target. Here we report the crystal structure of FP2 in complex with a protease inhibitor, cystatin. The FP2 stru ...

    Falcipain-2 (FP2), the major cysteine protease of the human malaria parasite Plasmodium falciparum, is a hemoglobinase and promising drug target. Here we report the crystal structure of FP2 in complex with a protease inhibitor, cystatin. The FP2 structure reveals two previously undescribed cysteine protease structural motifs, designated FP2(nose) and FP2(arm), in addition to details of the active site that will help focus inhibitor design. Unlike most cysteine proteases, FP2 does not require a prodomain but only the short FP2(nose) motif to correctly fold and gain catalytic activity. Our structure and mutagenesis data suggest a molecular basis for this unique mechanism by highlighting the functional role of two Tyr within FP2(nose) and a conserved Glu outside this motif. The FP2(arm) motif is required for hemoglobinase activity. The structure reveals topographic features and a negative charge cluster surrounding FP2(arm) that suggest it may serve as an exo-site for hemoglobin binding. Motifs similar to FP2(nose) and FP2(arm) are found only in related plasmodial proteases, suggesting that they confer malaria-specific functions.

    Organizational Affiliation: 

    Department of Pathology and the Sandler Center, San Francisco General Hospital, University of California, CA 94143, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
falcipain 2
A
241Plasmodium falciparumMutation(s): 4 
Find proteins for Q9N6S8 (Plasmodium falciparum)
Go to UniProtKB:  Q9N6S8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cystatin
I
111Gallus gallusMutation(s): 0 
Find proteins for P01038 (Gallus gallus)
Go to UniProtKB:  P01038
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.232 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 96.036α = 90.00
b = 96.036β = 90.00
c = 124.164γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2005-02-15 
  • Released Date: 2006-03-28 
  • Deposition Author(s): Wang, S.X.

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance