2YNC

Plasmodium vivax N-myristoyltransferase in complex with YnC12-CoA thioester.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Validation of N-Myristoyltransferase as an Antimalarial Drug Target Using an Integrated Chemical Biology Approach.

Wright, M.H.Clough, B.Rackham, M.D.Rangachari, K.Brannigan, J.A.Grainger, M.Moss, D.K.Bottrill, A.R.Heal, W.P.Broncel, M.Serwa, R.A.Brady, D.Mann, D.Leatherbarrow, R.J.Tewari, R.Wilkinson, A.J.Holder, A.A.Tate, E.W.

(2014) Nat.Chem. 6: 112

  • DOI: 10.1038/nchem.1830
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to cu ...

    Malaria is an infectious disease caused by parasites of the genus Plasmodium, which leads to approximately one million deaths per annum worldwide. Chemical validation of new antimalarial targets is urgently required in view of rising resistance to current drugs. One such putative target is the enzyme N-myristoyltransferase, which catalyses the attachment of the fatty acid myristate to protein substrates (N-myristoylation). Here, we report an integrated chemical biology approach to explore protein myristoylation in the major human parasite P. falciparum, combining chemical proteomic tools for identification of the myristoylated and glycosylphosphatidylinositol-anchored proteome with selective small-molecule N-myristoyltransferase inhibitors. We demonstrate that N-myristoyltransferase is an essential and chemically tractable target in malaria parasites both in vitro and in vivo, and show that selective inhibition of N-myristoylation leads to catastrophic and irreversible failure to assemble the inner membrane complex, a critical subcellular organelle in the parasite life cycle. Our studies provide the basis for the development of new antimalarials targeting N-myristoyltransferase.


    Organizational Affiliation

    1] Department of Chemistry, Imperial College London, London SW7 2AZ, UK [2] Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
A, B
384Plasmodium vivax (strain Salvador I)Mutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K1A2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE
C
384Plasmodium vivax (strain Salvador I)Mutation(s): 0 
EC: 2.3.1.97
Find proteins for A5K1A2 (Plasmodium vivax (strain Salvador I))
Go to UniProtKB:  A5K1A2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B, C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B, C
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
YNC
Query on YNC

Download SDF File 
Download CCD File 
A, B, C
TETRADEC-13-YNOIC ACID - COA THIOESTER
C35 H58 N7 O17 P3 S
YPDKCQHYDROOAS-QSGBVPJFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.450α = 90.00
b = 119.050β = 90.00
c = 176.730γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-15
    Type: Initial release
  • Version 1.1: 2014-02-05
    Type: Database references