4A3Y

Crystal structure of Raucaffricine glucosidase from ajmaline biosynthesis pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures of Alkaloid Biosynthetic Glucosidases Decode Substrate Specificity.

Xia, L.Ruppert, M.Wang, M.Panjikar, S.Lin, H.Rajendran, C.Barleben, L.Stockigt, J.

(2012) Acs Chem.Biol. 7: 226

  • DOI: 10.1021/cb200267w
  • Primary Citation of Related Structures:  3U57, 3U5U, 3U5Y
  • Also Cited By: 3ZJ6, 4ATD, 4ATL

  • PubMed Abstract: 
  • Two similar enzymes with different biosynthetic function in one species have evolved to catalyze two distinct reactions. X-ray structures of both enzymes help reveal their most important differences. The Rauvolfia alkaloid biosynthetic network harbor ...

    Two similar enzymes with different biosynthetic function in one species have evolved to catalyze two distinct reactions. X-ray structures of both enzymes help reveal their most important differences. The Rauvolfia alkaloid biosynthetic network harbors two O-glucosidases: raucaffricine glucosidase (RG), which hydrolyses raucaffricine to an intermediate downstream in the ajmaline pathway, and strictosidine glucosidase (SG), which operates upstream. RG converts strictosidine, the substrate of SG, but SG does not accept raucaffricine. Now elucidation of crystal structures of RG, inactive RG-E186Q mutant, and its complexes with ligands dihydro-raucaffricine and secologanin reveals that it is the "wider gate" of RG that allows strictosidine to enter the catalytic site, whereas the "slot-like" entrance of SG prohibits access by raucaffricine. Trp392 in RG and Trp388 in SG control the gate shape and acceptance of substrates. Ser390 directs the conformation of Trp392. 3D structures, supported by site-directed mutations and kinetic data of RG and SG, provide a structural and catalytic explanation of substrate specificity and deeper insights into O-glucosidase chemistry.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAUCAFFRICINE-O-BETA-D-GLUCOSIDASE
A, B
540Rauvolfia serpentinaGene Names: RG (VGT)
EC: 3.2.1.125, 2.4.1.219
Find proteins for Q9SPP9 (Rauvolfia serpentina)
Go to UniProtKB:  Q9SPP9
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.165 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 102.774α = 90.00
b = 127.329β = 90.00
c = 215.837γ = 90.00
Software Package:
Software NamePurpose
Auto-Rickshawphasing
XDSdata reduction
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-15
    Type: Initial release