Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Zymomonas mobilis

Experimental Data Snapshot

  • Resolution: 1.91 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Crystal structure of 1-deoxy-d-xylulose-5-phosphate reductoisomerase from Zymomonas mobilis at 1.9-A resolution.

Ricagno, S.Grolle, S.Bringer-Meyer, S.Sahm, H.Lindqvist, Y.Schneider, G.

(2004) Biochim Biophys Acta 1698: 37-44

  • DOI: https://doi.org/10.1016/j.bbapap.2003.10.006
  • Primary Citation of Related Structures:  
    1R0K, 1R0L

  • PubMed Abstract: 

    1-Deoxy-d-xylulose-5-phosphate reductoisomerase (DXR) is the second enzyme in the non-mevalonate pathway of isoprenoid biosynthesis. The structure of the apo-form of this enzyme from Zymomonas mobilis has been solved and refined to 1.9-A resolution, and that of a binary complex with the co-substrate NADPH to 2.7-A resolution. The subunit of DXR consists of three domains. Residues 1-150 form the NADPH binding domain, which is a variant of the typical dinucleotide-binding fold. The second domain comprises a four-stranded mixed beta-sheet, with three helices flanking the sheet. Most of the putative active site residues are located on this domain. The C-terminal domain (residues 300-386) folds into a four-helix bundle. In solution and in the crystal, the enzyme forms a homo-dimer. The interface between the two monomers is formed predominantly by extension of the sheet in the second domain. The adenosine phosphate moiety of NADPH binds to the nucleotide-binding fold in the canonical way. The adenine ring interacts with the loop after beta1 and with the loops between alpha2 and beta2 and alpha5 and beta5. The nicotinamide ring is disordered in crystals of this binary complex. Comparisons to Escherichia coli DXR show that the two enzymes are very similar in structure, and that the active site architecture is highly conserved. However, there are differences in the recognition of the adenine ring of NADPH in the two enzymes.

  • Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Division of Molecular Structural Biology, Karolinska Institutet, Scheelevagen 2, S-171-77 Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
1-deoxy-D-xylulose 5-phosphate reductoisomerase
A, B, C, D
388Zymomonas mobilisMutation(s): 0 
Gene Names: DXR
Find proteins for Q9X5F2 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Explore Q9X5F2 
Go to UniProtKB:  Q9X5F2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X5F2
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.91 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.7α = 90
b = 93.2β = 90.5
c = 98.6γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-07-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-10-03
    Changes: Data collection
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description