2V91

STRUCTURE OF STRICTOSIDINE SYNTHASE IN COMPLEX WITH STRICTOSIDINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structure Based Engineering of Strictosidine Synthase: Auxiliary for Alkaloid Libraries

Loris, E.A.Panjikar, S.Ruppert, M.Barleben, L.Unger, M.Schubel, H.Stoeckigt, J.

(2007) Chem Biol 14: 979

  • DOI: https://doi.org/10.1016/j.chembiol.2007.08.009
  • Primary Citation of Related Structures:  
    2V91

  • PubMed Abstract: 

    The highly substrate-specific strictosidine synthase (EC 4.3.3.2) catalyzes the biological Pictet-Spengler condensation between tryptamine and secologanin, leading to the synthesis of about 2000 monoterpenoid indole alkaloids in higher plants. The crystal structure of Rauvolfia serpentina strictosidine synthase (STR1) in complex with strictosidine has been elucidated here, allowing the rational site-directed mutation of the active center of STR1 and resulting in modulation of its substrate acceptance. Here, we report on the rational redesign of STR1 by generation of a Val208Ala mutant, further describing the influence on substrate acceptance and the enzyme-catalyzed synthesis of 10-methyl- and 10-methoxystrictosidines. Based on the addition of strictosidine to a crude strictosidine glucosidase preparation from Catharanthus cells, a combined chemoenzymatic approach to generating large alkaloid libraries for future pharmacological screenings is presented.


  • Organizational Affiliation

    Department of Pharmaceutical Biology, Institute of Pharmacy, Johannes Gutenberg-University Mainz, Staudingerweg 5, D-55099 Mainz, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STRICTOSIDINE SYNTHASE
A, B
302Rauvolfia serpentinaMutation(s): 0 
EC: 4.3.3.2 (PDB Primary Data), 3.5.99.13 (UniProt)
UniProt
Find proteins for P68175 (Rauvolfia serpentina)
Explore P68175 
Go to UniProtKB:  P68175
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68175
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: 3.01 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.177α = 90
b = 150.177β = 90
c = 121.707γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata 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: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description
  • Version 1.4: 2024-11-06
    Changes: Structure summary