PDBsum entry 1ipe

Oxidoreductase

PDB id: 1ipe

Contents

Protein chains

259 a.a. *

Ligands

NDP ×2

Waters ×61

* Residue conservation analysis

PDB id:

1ipe

Name:

Oxidoreductase

Title:

Tropinone reductase-ii complexed with NADPH

Structure:

Tropinone reductase-ii. Chain: a, b. Engineered: yes

Source:

Datura stramonium. Jimsonweed. Organism_taxid: 4076. Organ: cultured root. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.195 R-free: 0.268

Authors:

A.Yamashita,M.Endo,T.Higashi,T.Nakatsu,Y.Yamada,J.Oda,H.Kato,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

A.Yamashita et al. (2003). Capturing enzyme structure prior to reaction initiation: tropinone reductase-II-substrate complexes. Biochemistry, 42, 5566-5573. PubMed id: 12741812 DOI: 10.1021/bi0272712

Date:

09-May-01 Release date: 03-Jun-03

Protein chains

P50163  (TRN2_DATST) -  Tropinone reductase 2 from Datura stramonium

Seq: 260 a.a.

Struc: 259 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.236 - tropinone reductase Ii.
• Reaction: pseudotropine + NADP⁺ = tropinone + NADPH + H⁺

pseudotropine (Bound ligand (Het Group name = NDP) corresponds exactly) + NADP(+) = tropinone + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi0272712

Biochemistry 42:5566-5573 (2003)

PubMed id: 12741812

Capturing enzyme structure prior to reaction initiation: tropinone reductase-II-substrate complexes.

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

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 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.