1T1R

Crystal Structure of the Reductoisomerase Complexed with a Bisphosphonate

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystallographic Structures of Two Bisphosphonate:1-Deoxyxylulose-5-Phosphate Reductoisomerase Complexes

Yajima, S., Hara, K., Sanders, J.M., Yin, F., Ohsawa, K., Wiesner, J., Jomaa, H., Oldfield, E.

(2004) J.Am.Chem.Soc. 126: 10824-10825

  • DOI: 10.1021/ja040126m
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • We have obtained the single-crystal X-ray crystallographic structures of the bisphosphonates [(1-isoquinolinylamino)methylene]-1,1-bisphosphonate and [[(5-chloro-2-pyridinyl)amino]methylene]-1,1-bisphosphonate, bound to the enzyme 1-deoxyxylulose-5-p ...

    We have obtained the single-crystal X-ray crystallographic structures of the bisphosphonates [(1-isoquinolinylamino)methylene]-1,1-bisphosphonate and [[(5-chloro-2-pyridinyl)amino]methylene]-1,1-bisphosphonate, bound to the enzyme 1-deoxyxylulose-5-phosphate reductoisomerase (DXR, EC 1.1.1.267, also known as 2-C-methyl-d-erythritol-4-phosphate synthase), an important target for the development of antimalarial drugs. Our results indicate that both bisphosphonates bind into the fosmidomycin binding site. The aromatic groups are in a shallow hydrophobic pocket, and the phosphonate groups are involved in electrostatic interactions with Mg2+ or a cluster of carboxylic acid groups and lysine while the fosmidomycin phosphonate-binding site is occupied by a sulfate ion (as also observed in the DXR/NADP+ structure). The availability of these two new crystal structures opens up the possibility of the further development of bisphosphonates and related systems as DXR inhibitors and, potentially, as antiinfective agents.

    Organizational Affiliation: 

    Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo 156-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B
398Escherichia 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
IMB
Query on IMB
Download SDF File 
Download CCD File 
A, B
[(ISOQUINOLIN-1-YLAMINO)-PHOSPHONO-METHYL]-PHOSPHONIC ACID
(3-ISOQUINOLYLAMINE) METHYLENE-1,1-BISPHOSPHONATE
C10 H12 N2 O6 P2
JPVMIOWESIQIGB-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IMBIC50: 4000 nM (100) BINDINGDB
IMBIC50: 4000 nM BINDINGMOAD
IMBIC50: 4000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 182.381α = 90.00
b = 59.042β = 90.00
c = 86.978γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance