4N7B | pdb_00004n7b

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

• PDB DOI: https://doi.org/10.2210/pdb4N7B/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Plasmodium falciparum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-10-15 Released: 2013-11-20 
• Deposition Author(s): Rekittke, I., Jomaa, H., Ermler, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

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

• PubMed: 24188825 
• DOI: https://doi.org/10.1016/j.febslet.2013.10.029
• Primary Citation Related Structures: 
  4N7B


• 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-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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 64.06 kDa 
• Atom Count: 2,770 
• Modeled Residue Count: 318 
• Deposited Residue Count: 541 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LytB	A	541	Plasmodium falciparum	Mutation(s): 0  Gene Names: lytB EC: 1.17.7.4
UniProt
Find proteins for Q8I295 (Plasmodium falciparum (isolate 3D7)) Explore Q8I295  Go to UniProtKB:  Q8I295

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3S	B [auth A]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.195 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.177 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.96	α = 90
b = 115.96	β = 90
c = 76.93	γ = 120

Software Package:

Software Name	Purpose
SHARP	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Rekittke, I., Jomaa, H., Ermler, U.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2017-11-15
  Changes: Refinement description
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations