1JVS

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

Experimental Data Snapshot

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

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This is version 1.4 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan. yshun@nodai.ac.jp


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
400Escherichia coliMutation(s): 18 
EC: 1.1.1.267
UniProt
Find proteins for P45568 (Escherichia coli (strain K12))
Explore P45568 
Go to UniProtKB:  P45568
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP45568
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
SO4
Query on SO4
Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 182.16α = 90
b = 59.185β = 90
c = 87.236γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALAdata scaling
SOLVEphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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