3V1S

Scaffold tailoring by a newly detected Pictet-Spenglerase ac-tivity of strictosidine synthase (STR1): from the common tryp-toline skeleton to the rare piperazino-indole framework


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Literature

Scaffold Tailoring by a Newly Detected Pictet-Spenglerase Activity of Strictosidine Synthase: From the Common Tryptoline Skeleton to the Rare Piperazino-indole Framework

Wu, F.Zhu, H.Sun, L.Rajendran, C.Wang, M.Ren, X.Panjikar, S.Cherkasov, A.Zou, H.Stockigt, J.

(2012) J Am Chem Soc 134: 1498-1500

  • DOI: https://doi.org/10.1021/ja211524d
  • Primary Citation of Related Structures:  
    3V1S

  • PubMed Abstract: 

    The Pictet-Spenglerase strictosidine synthase (STR1) has been recognized as a key enzyme in the biosynthesis of some 2000 indole alkaloids in plants, some with high therapeutic value. In this study, a novel function of STR1 has been detected which allows for the first time a simple enzymatic synthesis of the strictosidine analogue 3 harboring the piperazino[1,2-a]indole (PI) scaffold and to switch from the common tryptoline (hydrogenated carboline) to the rare PI skeleton. Insight into the reaction is provided by X-ray crystal analysis and modeling of STR1 ligand complexes. STR1 presently provides exclusively access to 3 and can act as a source to generate by chemoenzymatic approaches libraries of this novel class of alkaloids which may have new biological activities. Synthetic or natural monoterpenoid alkaloids with the PI core have not been reported before.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Strictosidine synthase
A, B
322Rauvolfia serpentinaMutation(s): 0 
Gene Names: STR1
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.33 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.976α = 90
b = 150.976β = 90
c = 121.471γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-29
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary