Strictosidine synthase

 

Strictosidine synthase is an unusual six-bladed beta-propeller fold protein which catalyses the condensation of two precursor molecules, tryptamine and monoterpenoid secologanin to form strictosidine. This molecule is the generic starting material for the biosynthetic formation of monoterpenoid-derived indole alkaloids, many of which are known to have potent therapeutic characteristics, including anti-cancer properties.

 

Reference Protein and Structure

Sequence
P68175 UniProt (4.3.3.2) IPR004141 (Sequence Homologues) (PDB Homologues)
Biological species
Rauvolfia serpentina (serpentwood) Uniprot
PDB
2fp8 - Structure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family (2.3 Å) PDBe PDBsum 2fp8
Catalytic CATH Domains
2.120.10.30 CATHdb (see all for 2fp8)
Click To Show Structure

Enzyme Reaction (EC:4.3.3.2)

tryptaminium
CHEBI:57887ChEBI
+
(-)-secologanin
CHEBI:18002ChEBI
→
water
CHEBI:15377ChEBI
+
3alpha(S)-strictosidinium(1+)
CHEBI:58193ChEBI
Alternative enzyme names: Strictosidine synthetase, STR, 3-alpha-(S)-strictosidine tryptamine-lyase,

Enzyme Mechanism

Introduction

The enzyme catalyses the biological equivalent of the Pictet-Spengler reaction, a reaction used to form synthetic equivalents of indole alkaloids of pharmaceutical interest.

Catalytic Residues Roles

UniProt PDB* (2fp8)
Glu309 Glu309(287)A Acts as a general acid/base. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator, increase nucleophilicity
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, bimolecular nucleophilic addition, intermediate formation, overall reactant used, intramolecular elimination, schiff base formed, overall product formed, intramolecular nucleophilic addition, native state of enzyme regenerated, inferred reaction step

References

  1. Ma X et al. (2006), Plant Cell, 18, 907-920. The Structure of Rauvolfia serpentina Strictosidine Synthase Is a Novel Six-Bladed  -Propeller Fold in Plant Proteins. DOI:10.1105/tpc.105.038018. PMID:16531499.
  2. Klausen RS et al. (2017), J Am Chem Soc, 139, 12299-12309. Chiral Thioureas Promote Enantioselective Pictet-Spengler Cyclization by Stabilizing Every Intermediate and Transition State in the Carboxylic Acid-Catalyzed Reaction. DOI:10.1021/jacs.7b06811. PMID:28787140.
  3. Stöckigt J et al. (2008), Plant Physiol Biochem, 46, 340-355. 3D-Structure and function of strictosidine synthase – the key enzyme of monoterpenoid indole alkaloid biosynthesis. DOI:10.1016/j.plaphy.2007.12.011. PMID:18280746.

Step 1. Glu309 deprotonates the primary amine of tryptamine, initiating nucleophilic attack at the aldehyde group of secologanin.

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Catalytic Residues Roles

Residue Roles
Glu309(287)A increase nucleophilicity, hydrogen bond acceptor, proton acceptor

Chemical Components

proton transfer, ingold: bimolecular nucleophilic addition, intermediate formation, overall reactant used

Step 2. An internal proton rearrangement occurs.

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Catalytic Residues Roles

Residue Roles
Glu309(287)A hydrogen bond donor

Chemical Components

proton transfer, intermediate formation

Step 3. The secondary amine eliminates water, forming a Schiff base intermediate.

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Catalytic Residues Roles

Residue Roles
Glu309(287)A activator, hydrogen bond donor, proton donor

Chemical Components

proton transfer, ingold: intramolecular elimination, schiff base formed, overall product formed, intermediate formation

Step 4. The indole double bond attacks the imine, forming a carbon-carbon bond and a carbocation stabilised through conjugation.

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Catalytic Residues Roles

Residue Roles
Glu309(287)A hydrogen bond acceptor

Chemical Components

ingold: intramolecular nucleophilic addition, intermediate formation

Step 5. The Glu309 abstracts the proton alpha to the carbocation, forming a double bond.

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Catalytic Residues Roles

Residue Roles
Glu309(287)A activator, hydrogen bond acceptor, proton acceptor

Chemical Components

proton transfer, intermediate formation

Step 6. The secondary amide deprotonates Glu309, regenerating the active site. The active site is burried, preventing access of solvent molecules to the intermediates formed during the reaction. Therefore, the product is shown here as deprotonating the general base, to allow for further catalysis, rather than proton abstraction by a solvent molecule [PMID:18280746].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu309(287)A activator, hydrogen bond donor, proton donor

Chemical Components

proton transfer, native state of enzyme regenerated, inferred reaction step
Download: Image, Marvin File

Step 1. Glu309 deprotonates the primary amine of tryptamine, initiating nucleophilic attack at the aldehyde group of secologanin.

Step 2. An internal proton rearrangement occurs.

Step 3. The secondary amine eliminates water, forming a Schiff base intermediate.

Step 4. The indole double bond attacks the imine, forming a carbon-carbon bond and a carbocation stabilised through conjugation.

Step 5. The Glu309 abstracts the proton alpha to the carbocation, forming a double bond.

Step 6. The secondary amide deprotonates Glu309, regenerating the active site. The active site is burried, preventing access of solvent molecules to the intermediates formed during the reaction. Therefore, the product is shown here as deprotonating the general base, to allow for further catalysis, rather than proton abstraction by a solvent molecule [PMID:18280746].

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, James Willey