2AE2

TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 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

  • 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.USA 95: 4876


    Organizational Affiliation

    Institute for Chemical Research, Kyoto University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (TROPINONE REDUCTASE-II)
A, B
260Datura stramoniumMutation(s): 0 
Gene Names: TR2
EC: 1.1.1.236
Find proteins for P50163 (Datura stramonium)
Go to UniProtKB:  P50163
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTO
Query on PTO

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

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.172 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.600α = 90.00
b = 88.600β = 90.00
c = 338.300γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-02
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance