1JVS

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase; a target enzyme for antimalarial drugs

• PDB DOI: https://doi.org/10.2210/pdb1JVS/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2001-08-31 Released: 2002-10-09 
• Deposition Author(s): Yajima, S., Nonaka, T., Kuzuyama, T., Seto, H., Ohsawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.213 

Literature

Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with cofactors: implications of a flexible loop movement upon substrate binding.

Yajima, S., Nonaka, T., Kuzuyama, T., Seto, H., Ohsawa, K.

(2002) J Biochem 131: 313-317

• PubMed: 11872159 
• DOI: https://doi.org/10.1093/oxfordjournals.jbchem.a003105
• Primary Citation of Related Structures:  
  1JVS


• PubMed Abstract: 
  

  The key enzyme in the nonmevalonate pathway, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR), has been shown to be an effective target of antimalarial drugs. Here we report the crystal structure of DXR complexed with NADPH and a sulfate ion from Escherichia coli at 2.2 A resolution. The structure showed the presence of an extra domain, which is absent from other NADPH-dependent oxidoreductases, in addition to the conformation of catalytic residues and the substrate binding site. A flexible loop covering the substrate binding site plays an important role in the enzymatic reaction and the determination of substrate specificity.

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Organizational Affiliation: 

Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, 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: 90.4 kDa 
• Atom Count: 6,446 
• Modelled Residue Count: 798 
• Deposited Residue Count: 800 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1-deoxy-D-xylulose 5-phosphate reductoisomerase	A, B	400	Escherichia coli	Mutation(s): 18  EC: 1.1.1.267
UniProt
Find proteins for P45568 (Escherichia coli (strain K12)) Explore P45568  Go to UniProtKB:  P45568

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	D [auth A], F [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.213 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.16	α = 90
b = 59.185	β = 90
c = 87.236	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
SCALA	data scaling
SOLVE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-10-09 
Deposition Author(s): Yajima, S., Nonaka, T., Kuzuyama, T., Seto, H., Ohsawa, K.

Revision History  

• Version 1.0: 2002-10-09
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2019-11-06
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary