3AU9

Crystal structure of the quaternary complex-1 of an isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum

Umeda, T.Tanaka, N.Kusakabe, Y.Nakanishi, M.Kitade, Y.Nakamura, K.T.

(2011) Sci Rep 1: 9-9

  • DOI: 10.1038/srep00009
  • Primary Citation of Related Structures:  3AU8, 3AUA

  • PubMed Abstract: 
  • The human malaria parasite Plasmodium falciparum is responsible for the deaths of more than a million people each year. Fosmidomycin has been proven to be efficient in the treatment of P. falciparum malaria by inhibiting 1-deoxy-D-xylulose 5-phosphat ...

    The human malaria parasite Plasmodium falciparum is responsible for the deaths of more than a million people each year. Fosmidomycin has been proven to be efficient in the treatment of P. falciparum malaria by inhibiting 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), an enzyme of the non-mevalonate pathway, which is absent in humans. However, the structural details of DXR inhibition by fosmidomycin in P. falciparum are unknown. Here, we report the crystal structures of fosmidomycin-bound complete quaternary complexes of PfDXR. Our study revealed that (i) an intrinsic flexibility of the PfDXR molecule accounts for an induced-fit movement to accommodate the bound inhibitor in the active site and (ii) a cis arrangement of the oxygen atoms of the hydroxamate group of the bound inhibitor is essential for tight binding of the inhibitor to the active site metal. We expect the present structures to be useful guides for the design of more effective antimalarial compounds.


    Organizational Affiliation

    School of Pharmacy, Showa University, Tokyo 142-8555, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
488Plasmodium falciparumGene Names: DXR
EC: 1.1.1.267
Find proteins for O96693 (Plasmodium falciparum)
Go to UniProtKB:  O96693
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FOM
Query on FOM

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A, B
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
FOSMIDOMYCIN
C4 H10 N O5 P
GJXWDTUCERCKIX-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

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Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 51.181α = 90.00
b = 77.615β = 90.88
c = 110.727γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
REFMACrefinement
AMoREphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2013-06-12
    Type: Database references