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 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.4 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: https://doi.org/10.1105/tpc.106.045682
  • Primary Citation of Related Structures:  
    2JF6, 2JF7

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STRICTOSIDINE-O-BETA-D-GLUCOSIDASE
A, B
532Rauvolfia serpentinaMutation(s): 0 
EC: 3.2.1.105
UniProt
Find proteins for Q8GU20 (Rauvolfia serpentina)
Explore Q8GU20 
Go to UniProtKB:  Q8GU20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GU20
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
S55
Query on S55

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159α = 90
b = 159β = 90
c = 102.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Refinement description, Version format compliance
  • Version 1.2: 2012-05-16
    Changes: Other
  • Version 1.3: 2019-07-24
    Changes: Data collection
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description