2R9B

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.271 

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
  • Primary Citation of Related Structures:  
    2R9B

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasmepsin-2AB329Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: plasmepsin 2
EC: 3.4.23.39
Find proteins for P46925 (Plasmodium falciparum)
Explore P46925 
Go to UniProtKB:  P46925
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
peptide-based inhibitorCD8N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
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: 2.80 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.271 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 219.489α = 90
b = 69.032β = 102.85
c = 53.578γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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