2AE2

TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure of tropinone reductase-II complexed with NADP+ and pseudotropine at 1.9 A resolution: implication for stereospecific substrate binding and catalysis.

Yamashita, A.Kato, H.Wakatsuki, S.Tomizaki, T.Nakatsu, T.Nakajima, K.Hashimoto, T.Yamada, Y.Oda, J.

(1999) Biochemistry 38: 7630-7637

  • DOI: https://doi.org/10.1021/bi9825044
  • Primary Citation of Related Structures:  
    2AE2

  • PubMed Abstract: 

    Tropinone reductase-II (TR-II) catalyzes the NADPH-dependent reduction of the carbonyl group of tropinone to a beta-hydroxyl group. The crystal structure of TR-II complexed with NADP+ and pseudotropine (psi-tropine) has been determined at 1.9 A resolution. A seven-residue peptide near the active site, disordered in the unliganded structure, is fixed in the ternary complex by participation of the cofactor and substrate binding. The psi-tropine molecule is bound in an orientation which satisfies the product configuration and the stereochemical arrangement toward the cofactor. The substrate binding site displays a complementarity to the bound substrate (psi-tropine) in its correct orientation. In addition, electrostatic interactions between the substrate and Glu156 seem to specify the binding position and orientation of the substrate. A comparison between the active sites in TR-II and TR-I shows that they provide different van der Waals surfaces and electrostatic features. These differences likely contribute to the correct binding mode of the substrates, which are in opposite orientations in TR-II and TR-I, and to different reaction stereospecificities. The active site structure in the TR-II ternary complex also suggests that the arrangement of the substrate, cofactor, and catalytic residues is stereoelectronically favorable for the reaction.


  • Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (TROPINONE REDUCTASE-II)
A, B
260Datura stramoniumMutation(s): 0 
EC: 1.1.1.236
UniProt
Find proteins for P50163 (Datura stramonium)
Explore P50163 
Go to UniProtKB:  P50163
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50163
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.6α = 90
b = 88.6β = 90
c = 338.3γ = 120
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-02-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description