3T8V

A bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Bestatin-based chemical biology strategy reveals distinct roles for malaria M1- and M17-family aminopeptidases

Harbut, M.B.Velmourougane, G.Dalal, S.Reiss, G.Whisstock, J.C.Onder, O.Brisson, D.McGowan, S.Klemba, M.Greenbaum, D.C.

(2011) Proc Natl Acad Sci U S A 108: E526-E534

  • DOI: https://doi.org/10.1073/pnas.1105601108
  • Primary Citation of Related Structures:  
    3T8V, 3T8W

  • PubMed Abstract: 

    Malaria causes worldwide morbidity and mortality, and while chemotherapy remains an excellent means of malaria control, drug-resistant parasites necessitate the discovery of new antimalarials. Peptidases are a promising class of drug targets and perform several important roles during the Plasmodium falciparum erythrocytic life cycle. Herein, we report a multidisciplinary effort combining activity-based protein profiling, biochemical, and peptidomic approaches to functionally analyze two genetically essential P. falciparum metallo-aminopeptidases (MAPs), PfA-M1 and Pf-LAP. Through the synthesis of a suite of activity-based probes (ABPs) based on the general MAP inhibitor scaffold, bestatin, we generated specific ABPs for these two enzymes. Specific inhibition of PfA-M1 caused swelling of the parasite digestive vacuole and prevented proteolysis of hemoglobin (Hb)-derived oligopeptides, likely starving the parasite resulting in death. In contrast, inhibition of Pf-LAP was lethal to parasites early in the life cycle, prior to the onset of Hb degradation suggesting that Pf-LAP has an essential role outside of Hb digestion.


  • Organizational Affiliation

    Department of Pharmacology, University of Pennsylvania, 433 South University Avenue, 304G Lynch Laboratories, Philadelphia, PA 19104-6018, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M1 family aminopeptidase895Plasmodium falciparum FcB1/ColumbiaMutation(s): 8 
EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7))
Explore O96935 
Go to UniProtKB:  O96935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96935
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
BTJ PDBBind:  3T8V Ki: 260 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.542α = 90
b = 108.821β = 90
c = 118.274γ = 90
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-28
    Type: Initial release
  • Version 1.1: 2024-03-20
    Changes: Data collection, Database references, Derived calculations