2EGH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 63: 466-470

  • DOI: 10.1107/S1744309107024475

  • 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 pathwa ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
424Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: dxr (ispC, yaeM)
EC: 1.1.1.267
Find proteins for P45568 (Escherichia coli (strain K12))
Go to UniProtKB:  P45568
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
FOM
Query on FOM

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Download CCD File 
A, B
3-[FORMYL(HYDROXY)AMINO]PROPYLPHOSPHONIC ACID
FOSMIDOMYCIN
C4 H10 N O5 P
GJXWDTUCERCKIX-UHFFFAOYSA-N
 Ligand Interaction
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FOMIC50: 20 - 438 nM (100) BINDINGDB
FOMKi: 38 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 180.590α = 90.00
b = 59.115β = 90.00
c = 87.050γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
ADSCdata collection
CNSrefinement
CNSphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-19
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance