2EGH

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with a magnesium ion, NADPH and fosmidomycin

• PDB DOI: https://doi.org/10.2210/pdb2EGH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli str. K-12 substr. W3110
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-01 Released: 2007-06-19 
• Deposition Author(s): Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Seto, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase in a quaternary complex with a magnesium ion, NADPH and the antimalarial drug fosmidomycin

Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Ohsawa, K., Seto, H.

(2007) Acta Crystallogr Sect F Struct Biol Cryst Commun 63: 466-470

• PubMed: 17554164 
• DOI: https://doi.org/10.1107/S1744309107024475
• Primary Citation of Related Structures:  
  2EGH


• PubMed Abstract: 
  

  The crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) from Escherichia coli complexed with Mg(2+), NADPH and fosmidomycin was solved at 2.2 A resolution. DXR is the key enzyme in the 2-C-methyl-D-erythritol 4-phosphate pathway and is an effective target of antimalarial drugs such as fosmidomycin. In the crystal structure, electron density for the flexible loop covering the active site was clearly observed, indicating the well ordered conformation of DXR upon substrate binding. On the other hand, no electron density was observed for the nicotinamide-ribose portion of NADPH and the position of Asp149 anchoring Mg(2+) was shifted by NADPH in the active site.

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Organizational Affiliation: 

Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 94.25 kDa 
• Atom Count: 6,482 
• Modelled Residue Count: 798 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	424	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0  Gene Names: dxr EC: 1.1.1.267
UniProt
Find proteins for P45568 (Escherichia coli (strain K12)) Explore P45568  Go to UniProtKB:  P45568

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], H [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
FOM	D [auth A], G [auth B]	3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID C4 H10 N O5 P GJXWDTUCERCKIX-UHFFFAOYSA-N
MG	C [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FOM	BindingDB:  2EGH	IC50: min: 20, max: 438 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.218 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 180.59	α = 90
b = 59.115	β = 90
c = 87.05	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-06-19 
Deposition Author(s): Yajima, S., Hara, K., Iino, D., Sasaki, Y., Kuzuyama, T., Seto, H.

Revision History  

• Version 1.0: 2007-06-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description