1IPF

TROPINONE REDUCTASE-II COMPLEXED WITH NADPH AND TROPINONE

Summary for 1IPF

• Entry DOI: 10.2210/pdb1ipf/pdb
• Related: 1IPE
• Descriptor: TROPINONE REDUCTASE-II, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, 8-METHYL-8-AZABICYCLO[3,2,1]OCTAN-3-ONE, ... (4 entities in total)
• Functional Keywords: oxidoreductase, tropane alkaloid biosynthesis, reduction of tropinone to pseudotropine, short-chain dehydrogenase, tropinone, laue diffraction, riken structural genomics/proteomics initiative, rsgi, structural genomics
• Biological source: Datura stramonium (jimsonweed)
• Total number of polymer chains: 2
• Total formula weight: 58185.73

Authors

Yamashita, A.,Endo, M.,Higashi, T.,Nakatsu, T.,Yamada, Y.,Oda, J.,Kato, H.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2001-05-09, release date: 2003-06-03, Last modification date: 2023-10-25)

Primary citation

Yamashita, A.,Endo, M.,Higashi, T.,Nakatsu, T.,Yamada, Y.,Oda, J.,Kato, H.
Capturing Enzyme Structure Prior to Reaction Initiation: Tropinone Reductase-II-Substrate Complexes
BIOCHEMISTRY, 42:5566-5573, 2003

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 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.

PubMed: 12741812
DOI: 10.1021/bi0272712

Experimental method

X-RAY DIFFRACTION (2.5 Å)