1IPE

TROPINONE REDUCTASE-II COMPLEXED WITH NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes

Yamashita, A.Endo, M.Higashi, T.Nakatsu, T.Yamada, Y.Oda, J.Kato, H.

(2003) BIOCHEMISTRY 42: 5566-5573

  • DOI: 10.1021/bi0272712
  • Primary Citation of Related Structures:  1IPF

  • PubMed Abstract: 
  • To understand the catalytic mechanism of an enzyme, it is crucial to determine the crystallographic structures corresponding to the individual reaction steps. Here, we report two crystal structures of enzyme-substrate complexes prior to reaction init ...

    To understand the catalytic mechanism of an enzyme, it is crucial to determine the crystallographic structures corresponding to the individual reaction steps. Here, we report two crystal structures of enzyme-substrate complexes prior to reaction initiation: tropinone reductase-II (TR-II)-NADPH and TR-II-NADPH-tropinone complexes, determined from the identical crystals. A combination of two kinetic crystallographic techniques, a continuous flow of the substrates and Laue diffraction measurements, enabled us to capture the transit structures prior to the reaction proceeding. A structure comparison of the enzyme-substrate complex elucidated in this study with the enzyme-product complex in our previous study indicates that one of the substrates, tropinone, is rotated relative to the product so as to make the spatial organization in the active site favorable for the reaction to proceed. Side chains of the residues in the active site also alter their conformations to keep the complementarity of the space for the substrate or the product and to assist the rotational movement.


    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
    • 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


    Organizational Affiliation

    Structural Biochemistry Laboratory, RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo 679-5148, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TROPINONE REDUCTASE-II
A, B
259Datura stramoniumGene Names: TR2
EC: 1.1.1.236
Find proteins for P50163 (Datura stramonium)
Go to UniProtKB:  P50163
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download SDF File 
Download CCD File 
A, B
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.195 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.600α = 90.00
b = 88.600β = 90.00
c = 338.900γ = 120.00
Software Package:
Software NamePurpose
LAUENORMdata reduction
X-PLORrefinement
X-PLORmodel building
LAUENORMdata scaling
X-PLORphasing
INTLAUEdata reduction
INTLAUEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance