2R9B

Structural Analysis of Plasmepsin 2 from Plasmodium falciparum complexed with a peptide-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Recombinant plasmepsin 1 from the human malaria parasite plasmodium falciparum: enzymatic characterization, active site inhibitor design, and structural analysis.

Liu, P.Marzahn, M.R.Robbins, A.H.Gutierrez-de-Teran, H.Rodriguez, D.McClung, S.H.Stevens, S.M.Yowell, C.A.Dame, J.B.McKenna, R.Dunn, B.M.

(2009) Biochemistry 48: 4086-4099

  • DOI: 10.1021/bi802059r

  • PubMed Abstract: 
  • A mutated form of truncated proplasmepsin 1 (proPfPM1) from the human malaria parasite Plasmodium falciparum, proPfPM1 K110pN, was generated and overexpressed in Escherichia coli. The automaturation process was carried out at pH 4.0 and 4.5, and the ...

    A mutated form of truncated proplasmepsin 1 (proPfPM1) from the human malaria parasite Plasmodium falciparum, proPfPM1 K110pN, was generated and overexpressed in Escherichia coli. The automaturation process was carried out at pH 4.0 and 4.5, and the optimal catalytic pH of the resulting mature PfPM1 was determined to be pH 5.5. This mature PfPM1 showed comparable binding affinity to peptide substrates and inhibitors with the naturally occurring form isolated from parasites. The S3-S3' subsite preferences of the recombinant mature PfPM1 were explored using combinatorial chemistry based peptide libraries. On the basis of the results, a peptidomimetic inhibitor (compound 1) was designed and yielded 5-fold selectivity for binding to PfPM1 versus the homologous human cathepsin D (hcatD). The 2.8 A structure of the PfPM2-compound 1 complex is reported. Modeling studies were conducted using a series of peptidomimetic inhibitors (compounds 1-6, Table 3) and three plasmepsins: the crystal structure of PfPM2, and homology derived models of PfPM1 and PfPM4.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida 32610-0245, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Plasmepsin-2
A, B
329Plasmodium falciparumMutation(s): 0 
EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Go to UniProtKB:  P46925
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
peptide-based inhibitor
C, D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000306
Query on PRD_000306
C,DKPFS-(CH2-NH)-LQF peptidomimetic inhibitor of PfPM1Peptide-like / Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 219.489α = 90.00
b = 69.032β = 102.85
c = 53.578γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
CrystalCleardata collection
DENZOdata reduction
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2011-08-17
    Type: Non-polymer description
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-10-25
    Type: Refinement description