Tuberculosinol synthase

 

This enzyme is responsible for the conversion of tuberculosinyl diphosphate to tuberculosinol and the R and S iso-tuberculosinols. Tuberculosinols are one class of virulence factor in Mycobacterium tuberculosis. The active site for both of these functions is the same, but the R- and S-iso-tuberculosinol formation involves the addition of water at the C13 atom, rather than the C15, and involve an allylic rearrangement.

 

Reference Protein and Structure

Sequence
P9WJ61 UniProt (2.5.1.153) IPR001441 (Sequence Homologues) (PDB Homologues)
Biological species
Mycobacterium tuberculosis H37Rv (Bacteria) Uniprot
PDB
3wql - Crystal structure of Rv3378c with Mg2+ and PPi (2.1 Å) PDBe PDBsum 3wql
Catalytic CATH Domains
3.40.1180.10 CATHdb (see all for 3wql)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:3.1.7.8)

water
CHEBI:15377ChEBI
+
tuberculosinyl diphosphate(3-)
CHEBI:58822ChEBI
→
tuberculosinol
CHEBI:50387ChEBI
+
diphosphate(3-)
CHEBI:33019ChEBI
Alternative enzyme names: Rv3378c,

Enzyme Mechanism

Introduction

This mechanism proposal represents the primary product of this enzyme. Tyr51 abstracts a proton from the catalytic water, which attacks the C15 position and eliminates the diphosphate group.

Catalytic Residues Roles

UniProt PDB* (3wql)
Tyr51 Tyr51B Acts as a general acid/base. proton acceptor, proton donor
Asp34 Asp34B Forms part of the magnesium binding site. metal ligand
*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, overall reactant used, overall product formed, bimolecular nucleophilic substitution, inferred reaction step, native state of enzyme regenerated

References

  1. Chan HC et al. (2014), J Am Chem Soc, 136, 2892-2896. Structure and inhibition of tuberculosinol synthase and decaprenyl diphosphate synthase from Mycobacterium tuberculosis. DOI:10.1021/ja413127v. PMID:24475925.
  2. Nakano C et al. (2011), Biosci Biotechnol Biochem, 75, 75-81. Characterization of the Rv3378c gene product, a new diterpene synthase for producing tuberculosinol and (13R, S)-isotuberculosinol (nosyberkol), from the Mycobacterium tuberculosis H37Rv genome. DOI:10.1271/bbb.100570. PMID:21228491.

Step 1. Tyr51 abstracts a proton from the catalytic water, which attacks the C15 position and eliminates the diphosphate group.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp34B metal ligand
Tyr51B proton acceptor

Chemical Components

proton transfer, overall reactant used, overall product formed, ingold: bimolecular nucleophilic substitution

Step 2. In an inferred return step, the product diphosphate abstracts a proton from Tyr51.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp34B metal ligand
Tyr51B proton donor

Chemical Components

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

Step 1. Tyr51 abstracts a proton from the catalytic water, which attacks the C15 position and eliminates the diphosphate group.

Step 2. In an inferred return step, the product diphosphate abstracts a proton from Tyr51.

Products.

Contributors

Gemma L. Holliday