3EBH

Structure of the M1 Alanylaminopeptidase from malaria complexed with bestatin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the inhibition of the essential Plasmodium falciparum M1 neutral aminopeptidase

McGowan, S.Porter, C.J.Lowther, J.Stack, C.M.Golding, S.J.Skinner-Adams, T.S.Trenholme, K.R.Teuscher, F.Donnelly, S.M.Grembecka, J.Mucha, A.Kafarski, P.Degori, R.Buckle, A.M.Gardiner, D.L.Whisstock, J.C.Dalton, J.P.

(2009) Proc.Natl.Acad.Sci.USA 106: 2537-2542

  • DOI: 10.1073/pnas.0807398106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in >2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for th ...

    Plasmodium falciparum parasites are responsible for the major global disease malaria, which results in >2 million deaths each year. With the rise of drug-resistant malarial parasites, novel drug targets and lead compounds are urgently required for the development of new therapeutic strategies. Here, we address this important problem by targeting the malarial neutral aminopeptidases that are involved in the terminal stages of hemoglobin digestion and essential for the provision of amino acids used for parasite growth and development within the erythrocyte. We characterize the structure and substrate specificity of one such aminopeptidase, PfA-M1, a validated drug target. The X-ray crystal structure of PfA-M1 alone and in complex with the generic inhibitor, bestatin, and a phosphinate dipeptide analogue with potent in vitro and in vivo antimalarial activity, hPheP[CH(2)]Phe, reveals features within the protease active site that are critical to its function as an aminopeptidase and can be exploited for drug development. These results set the groundwork for the development of antimalarial therapeutics that target the neutral aminopeptidases of the parasite.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology and Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton, Victoria, 3800, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
M1 family aminopeptidase
A
889Plasmodium falciparumMutation(s): 7 
EC: 3.4.11.-
Find proteins for O96935 (Plasmodium falciparum)
Go to UniProtKB:  O96935
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
BES
Query on BES

Download SDF File 
Download CCD File 
A
2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
BESTATIN
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BESKi: 190 nM (99) BINDINGDB
BESIC50: 284 nM (99) BINDINGDB
BESKi: 478 nM BINDINGMOAD
BESKi: 478 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 75.651α = 90.00
b = 108.628β = 90.00
c = 117.964γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance