2VAQ image
Deposition Date 2007-09-04
Release Date 2008-09-16
Last Version Date 2024-10-16
Entry Detail
PDB ID:
2VAQ
Keywords:
Title:
STRUCTURE OF STRICTOSIDINE SYNTHASE IN COMPLEX WITH INHIBITOR
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
3.01 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
H 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:STRICTOSIDINE SYNTHASE
Gene (Uniprot):STR1
Chain IDs:A, B
Chain Length:322
Number of Molecules:2
Biological Source:RAUVOLFIA SERPENTINA
Ligand Molecules
Primary Citation
Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme.
J. Am. Chem. Soc. 130 710 723 (2008)
PMID: 18081287 DOI: 10.1021/ja077190z

Abstact

The Pictet-Spengler reaction, which yields either a beta-carboline or a tetrahydroquinoline product from an aromatic amine and an aldehyde, is widely utilized in plant alkaloid biosynthesis. Here we deconvolute the role that the biosynthetic enzyme strictosidine synthase plays in catalyzing the stereoselective synthesis of a beta-carboline product. Notably, the rate-controlling step of the enzyme mechanism, as identified by the appearance of a primary kinetic isotope effect (KIE), is the rearomatization of a positively charged intermediate. The KIE of a nonenzymatic Pictet-Spengler reaction indicates that rearomatization is also rate-controlling in solution, suggesting that the enzyme does not significantly change the mechanism of the reaction. Additionally, the pH dependence of the solution and enzymatic reactions provides evidence for a sequence of acid-base catalysis steps that catalyze the Pictet-Spengler reaction. An additional acid-catalyzed step, most likely protonation of a carbinolamine intermediate, is also significantly rate controlling. We propose that this step is efficiently catalyzed by the enzyme. Structural analysis of a bisubstrate inhibitor bound to the enzyme suggests that the active site is exquisitely tuned to correctly orient the iminium intermediate for productive cyclization to form the diastereoselective product. Furthermore, ab initio calculations suggest the structures of possible productive transition states involved in the mechanism. Importantly, these calculations suggest that a spiroindolenine intermediate, often invoked in the Pictet-Spengler mechanism, does not occur. A detailed mechanism for enzymatic catalysis of the beta-carboline product is proposed from these data.

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Primary Citation of related structures