3V0T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.333 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of perakine reductase, founding member of a novel aldo-keto reductase (AKR) subfamily that undergoes unique conformational changes during NADPH binding.

Sun, L.Chen, Y.Rajendran, C.Mueller, U.Panjikar, S.Wang, M.Mindnich, R.Rosenthal, C.Penning, T.M.Stockigt, J.

(2012) J.Biol.Chem. 287: 11213-11221

  • DOI: 10.1074/jbc.M111.335521
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 t ...

    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 Å. 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 Å. Overall, PR folds in an unusual α(8)/β(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 β-strands in the C terminus become ordered to form one α-helix, and a movement of up to 24 Å 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.


    Organizational Affiliation

    Institute of Materia Medica, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Perakine Reductase
A
337Rauvolfia serpentinaMutation(s): 1 
Gene Names: PR
EC: 1.1.1.317
Find proteins for Q3L181 (Rauvolfia serpentina)
Go to UniProtKB:  Q3L181
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATR
Query on ATR

Download SDF File 
Download CCD File 
A
2'-MONOPHOSPHOADENOSINE-5'-DIPHOSPHATE
C10 H16 N5 O13 P3
YPTPYQSAVGGMFN-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.333 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.215 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.501α = 90.00
b = 54.501β = 90.00
c = 200.358γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references