7RY7

Structure of Plasmepsin X (PM10, PMX) from Plasmodium falciparum 3D7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the zymogen and molecular basis for binding of inhibitors in mature enzyme.

Kesari, P.Deshmukh, A.Pahelkar, N.Suryawanshi, A.B.Rathore, I.Mishra, V.Dupuis, J.H.Xiao, H.Gustchina, A.Abendroth, J.Labaied, M.Yada, R.Y.Wlodawer, A.Edwards, T.E.Lorimer, D.D.Bhaumik, P.

(2022) Protein Sci 31: 882-899

  • DOI: https://doi.org/10.1002/pro.4279
  • Primary Citation of Related Structures:  
    7RY7

  • PubMed Abstract: 

    Plasmodium falciparum plasmepsin X (PfPMX), involved in the invasion and egress of this deadliest malarial parasite, is essential for its survival and hence considered as an important drug target. We report the first crystal structure of PfPMX zymogen containing a novel fold of its prosegment. A unique twisted loop from the prosegment and arginine 244 from the mature enzyme is involved in zymogen inactivation; such mechanism, not previously reported, might be common for apicomplexan proteases similar to PfPMX. The maturation of PfPMX zymogen occurs through cleavage of its prosegment at multiple sites. Our data provide thorough insights into the mode of binding of a substrate and a potent inhibitor 49c to PfPMX. We present molecular details of inactivation, maturation, and inhibition of PfPMX that should aid in the development of potent inhibitors against pepsin-like aspartic proteases from apicomplexan parasites.


  • Organizational Affiliation

    Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Plasmepsin X467Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0808200
EC: 3.4.23.1
UniProt
Find proteins for Q8IAS0 (Plasmodium falciparum (isolate 3D7))
Explore Q8IAS0 
Go to UniProtKB:  Q8IAS0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IAS0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 192.3α = 90
b = 50.88β = 93.149
c = 49.92γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MR-Rosettaphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHHSN272201700059C

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-30
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description