1K5H

1-deoxy-D-xylulose-5-phosphate reductoisomerase

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


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

Literature

Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis.

Reuter, K., Sanderbrand, S., Jomaa, H., Wiesner, J., Steinbrecher, I., Beck, E., Hintz, M., Klebe, G., Stubbs, M.T.

(2002) J.Biol.Chem. 277: 5378-5384

  • DOI: 10.1074/jbc.M109500200

  • PubMed Abstract: 

    • We have solved the 2.5-A crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, an enzyme involved in the mevalonate-independent 2-C-methyl-D-erythritol-4-phosphate pathway of isoprenoid biosynthesis. The structure reveals that the enz ...

    We have solved the 2.5-A crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, an enzyme involved in the mevalonate-independent 2-C-methyl-D-erythritol-4-phosphate pathway of isoprenoid biosynthesis. The structure reveals that the enzyme is present as a homodimer. Each monomer displays a V-like shape and is composed of an amino-terminal dinucleotide binding domain, a connective domain, and a carboxyl-terminal four-helix bundle domain. The connective domain is responsible for dimerization and harbors most of the active site. The strictly conserved acidic residues Asp(150), Glu(152), Glu(231), and Glu(234) are clustered at the putative active site and are probably involved in the binding of divalent cations mandatory for enzyme activity. The connective and four-helix bundle domains show significant mobility upon superposition of the dinucleotide binding domains of the three conformational states present in the asymmetric unit of the crystal. A still more pronounced flexibility is observed for a loop spanning residues 186 to 216, which adopts two completely different conformations within the three protein conformers. A possible involvement of this loop in an induced fit during substrate binding is discussed.

    Organizational Affiliation: 

    Institut für Pharmazeutische Chemie, Philipps-Universität, Marbacher Weg 6, D-35032 Marburg, Germany. reuterk@mailer.uni-marburg.de




Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
1-deoxy-D-xylulose-5-phosphate reductoisomerase
A, B, C
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.266α = 90.00
b = 249.263β = 90.00
c = 132.112γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
SOLVEphasing
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-02-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance