3UYI: Crystal Structure of Perakine Reductase, Founder Member of a Novel AKR Subfamily with Unique Conformational Changes during NADPH Binding

Perakine reductase (PR) catalyzes the NADPH-dependent reduction of the aldehyde perakine to yield the alcohol raucaffrinoline in the biosynthetic pathway of ajmaline in Rauvolfia, a key step in indole alkaloid biosynthesis. Sequence alignment shows that PR is the founder of the new AKR13D subfamily and is designated AKR13D1. The x-ray structure of methylated His(6)-PR was solved to 2.31 A. However, the active site of PR was blocked by the connected parts of the neighbor symmetric molecule in the crystal. To break the interactions and obtain the enzyme-ligand complexes, the A213W mutant was generated. The atomic structure of His(6)-PR-A213W complex with NADPH was determined at 1.77 A. Overall, PR folds in an unusual alpha(8)/beta(6) barrel that has not been observed in any other AKR protein to date. NADPH binds in an extended pocket, but the nicotinamide riboside moiety is disordered. Upon NADPH binding, dramatic conformational changes and movements were observed: two additional beta-strands in the C terminus become ordered to form one alpha-helix, and a movement of up to 24 A occurs. This conformational change creates a large space that allows the binding of substrates of variable size for PR and enhances the enzyme activity; as a result cooperative kinetics are observed as NADPH is varied. As the founding member of the new AKR13D subfamily, PR also provides a structural template and model of cofactor binding for the AKR13 family.
PDB ID: 3UYIDownload
MMDB ID: 97452
PDB Deposition Date: 2011/12/6
Updated in MMDB: 2018/07
Experimental Method:
x-ray diffraction
Resolution: 2.313  Å
Source Organism:
Similar Structures:
Biological Unit for 3UYI: dimeric; determined by author and by software (PISA)
Molecular Components in 3UYI
Label Count Molecule
Proteins (2 molecules)
Perakine Reductase
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB