Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 

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Crystal structures of two tropinone reductases: different reaction stereospecificities in the same protein fold.

Nakajima, K.Yamashita, A.Akama, H.Nakatsu, T.Kato, H.Hashimoto, T.Oda, J.Yamada, Y.

(1998) Proc Natl Acad Sci U S A 95: 4876-4881

  • DOI: https://doi.org/10.1073/pnas.95.9.4876
  • Primary Citation of Related Structures:  
    1AE1, 2AE1

  • PubMed Abstract: 

    A pair of tropinone reductases (TRs) share 64% of the same amino acid residues and belong to the short-chain dehydrogenase/reductase family. In the synthesis of tropane alkaloids in several medicinal plants, the TRs reduce a carbonyl group of an alkaloid intermediate, tropinone, to hydroxy groups with different diastereomeric configurations. To clarify the structural basis for their different reaction stereospecificities, we determined the crystal structures of the two enzymes at 2.4- and 2.3-A resolutions. The overall folding of the two enzymes was almost identical. The conservation was not confined within the core domains that are conserved within the protein family but extended outside the core domain where each family member has its characteristic structure. The binding sites for the cofactor and the positions of the active site residues were well conserved between the two TRs. The substrate binding site was composed mostly of hydrophobic amino acids in both TRs, but the presence of different charged residues conferred different electrostatic environments on the two enzymes. A modeling study indicated that these charged residues play a major role in controlling the binding orientation of tropinone within the substrate binding site, thereby determining the stereospecificity of the reaction product. The results obtained herein raise the possibility that in certain cases different stereospecificities can be acquired in enzymes by changing a few amino acid residues within substrate binding sites.

  • Organizational Affiliation

    Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan. k-nakji@bs.aist-nara.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
273Datura stramoniumMutation(s): 0 
Find proteins for P50162 (Datura stramonium)
Explore P50162 
Go to UniProtKB:  P50162
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50162
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C21 H28 N7 O17 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.155 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.74α = 90
b = 122.75β = 90
c = 75.51γ = 90
Software Package:
Software NamePurpose
PROCESSdata reduction
PROCESSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-11-18
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations