2JF6

Structure of inactive mutant of Strictosidine Glucosidase in complex with strictosidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Architecture of Strictosidine Glucosidase - the Gateway to the Biosynthesis of the Monoterpenoid Indole Alkaloid Family

Barleben, L.Panjikar, S.Ruppert, M.Koepke, J.Stockigt, J.

(2007) Plant Cell 19: 2886

  • DOI: 10.1105/tpc.106.045682
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Strictosidine beta-D-glucosidase (SG) follows strictosidine synthase (STR1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. This family is composed of approxim ...

    Strictosidine beta-D-glucosidase (SG) follows strictosidine synthase (STR1) in the production of the reactive intermediate required for the formation of the large family of monoterpenoid indole alkaloids in plants. This family is composed of approximately 2000 structurally diverse compounds. SG plays an important role in the plant cell by activating the glucoside strictosidine and allowing it to enter the multiple indole alkaloid pathways. Here, we report detailed three-dimensional information describing both native SG and the complex of its inactive mutant Glu207Gln with the substrate strictosidine, thus providing a structural characterization of substrate binding and identifying the amino acids that occupy the active site surface of the enzyme. Structural analysis and site-directed mutagenesis experiments demonstrate the essential role of Glu-207, Glu-416, His-161, and Trp-388 in catalysis. Comparison of the catalytic pocket of SG with that of other plant glucosidases demonstrates the structural importance of Trp-388. Compared with all other glucosidases of plant, bacterial, and archaeal origin, SG's residue Trp-388 is present in a unique structural conformation that is specific to the SG enzyme. In addition to STR1 and vinorine synthase, SG represents the third structural example of enzymes participating in the biosynthetic pathway of the Rauvolfia alkaloid ajmaline. The data presented here will contribute to deciphering the structure and reaction mechanism of other higher plant glucosidases.


    Organizational Affiliation

    Department of Pharmaceutical Biology, Institute of Pharmacy, Johanes Gutenberg-University, D-55099, Mainz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
A, B
532Rauvolfia serpentinaGene Names: SGR1
EC: 3.2.1.105
Find proteins for Q8GU20 (Rauvolfia serpentina)
Go to UniProtKB:  Q8GU20
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
S55
Query on S55

Download SDF File 
Download CCD File 
A, B
METHYL (2S,3R,4S)-3-ETHYL-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-[(1S)-2,3,4,9-TETRAHYDRO-1H-BETA-CARBOLIN-1-YLMETHYL]-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE
C27 H36 N2 O9
HZZMXWZOTXPILK-NTXHKPOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.000α = 90.00
b = 159.000β = 90.00
c = 102.900γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Refinement description, Version format compliance
  • Version 1.2: 2012-05-16
    Type: Other