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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 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 resol ...

    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.


    Related Citations: 
    • 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

    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (TROPINONE REDUCTASE-II)AB260Datura stramoniumMutation(s): 0 
Gene Names: TR2
EC: 1.1.1.236
Find proteins for P50163 (Datura stramonium)
Explore P50163 
Go to UniProtKB:  P50163
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
PTO
Query on PTO

Download CCD File 
A, B
PSEUDOTROPINE
C8 H15 N O
CYHOMWAPJJPNMW-RNLVFQAGSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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