4N7B

Structure of the E-1-hydroxy-2-methyl-but-2-enyl-4-diphosphate reductase from Plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.198 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase from Plasmodium falciparum.

Rekittke, I.Olkhova, E.Wiesner, J.Demmer, U.Warkentin, E.Jomaa, H.Ermler, U.

(2013) Febs Lett. 587: 3968-3972

  • DOI: 10.1016/j.febslet.2013.10.029

  • PubMed Abstract: 
  • Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-bu ...

    Terpenoid precursor biosynthesis occurs in human and many pathogenic organisms via the mevalonate and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, respectively. We determined the X-ray structure of the Fe/S containing (E)-4-hydroxy-3-methyl-but-2-enyl-diphosphate reductase (LytB) of the pathogenic protozoa Plasmodium falciparum which catalyzes the terminal step of the MEP pathway. The cloverleaf fold and the active site of P. falciparum LytB corresponds to those of the Aquifex aeolicus and Escherichia coli enzymes. Its distinct electron donor [2Fe-2S] ferredoxin was modeled to its binding site by docking calculations. The presented structural data provide a platform for a rational search of anti-malarian drugs.


    Organizational Affiliation

    Medizinische Klinik IV (Hämatologie), Justus-Liebig-Universität Giessen, Klinikstrasse 33, D-35392 Giessen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LytB
A
541Plasmodium falciparumMutation(s): 0 
Gene Names: lytB
Find proteins for Q9BJX6 (Plasmodium falciparum)
Go to UniProtKB:  Q9BJX6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F3S
Query on F3S

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A
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.198 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.172 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.960α = 90.00
b = 115.960β = 90.00
c = 76.930γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SHARPphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description