DOI: 10.5281/zenodo.17313803
title: MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases V1.0

description: A manualy curated specialized enzyme dataset of characterized terpene synthases and isoprenyl diphosphate synthases covering all the major terpene types, classes and taxonomic kingdoms. The dataset also covers known reaction mechanisms of terpene synthases described as cascades of individual reaction steps. 

The dataset can be browsed and accesed from a dediacated web page https://www.marts-db.org/. The Help page provides a detailed description of all fields within the dataset as well as the curation process. The web page also allows for downloads and user submissions of new data.

The file "reactions.csv" describes reactions catalyzed by enzymes within the dataset. The file "mechanisms.csv" describe individual reaction steps of reaction mechanisms.

Following is the data dictionary as described on the database web page. MARTS ID is an internal persistent identifier of enzymes, molecules and reaction mechanisms in the MARTS-DB.

Reactions.csv Every line is one reaction:




Column
Content




Enzyme_marts_ID
Marts ID of the enzyme.


Uniprot_ID
UniProt ID for enzymes that have a UniProt record.


Genbank_ID
Record of the protein transcript in GenBank, if it exists.


Enzyme_name
A descriptive name of the protein.


Aminoacid_sequence
The entire amino acid sequence of the protein.


Species
The species the enzyme was isolated from.


Kingdom
A broader taxonomic group of this species. Kingdoms have been split into groups of interest. Those groups are always written in brackets like animalia(corals).


Type
The type of the reaction. In terpene synthase reactions, type means the type of the terpene product, which is the number of carbons. The type is written as an abbreviation, e.g., mono for monoterpenes or di for diterpenes. Sesquiterpenes are abbreviated as sesq. Since isoprenyl diphosphate synthases and squalene synthases are also included, their type is given as pt, abbreviation of prenyl transferases.


Class
The class of the reaction. Terpene synthase reactions are divided into class I and class II reactions based on the initiation of the reaction cascade. Class I reactions are initiated by abstraction of a pyrophosphate, while class II by protonation of an alkyl or epoxide bond.


Substrate_name
The commonly used name of the substrate.


Substrate_smiles
The SMILES representation of the substrate. All diphosphates are written as oxoanions with charge on the diphosphate group.


Substrate_chebi_ID
The ChEBI ID of the substrate.


Substrate_marts_ID
The MARTS ID of the substrate.


Product_name
The commonly used name of the product.


Product_smiles
The SMILES representation of the product. All diphosphates are written as oxoanions with charge on the diphosphate group.


Product_chebi_ID
The ChEBI ID of the product.


Product_marts_ID
The MARTS ID of the product.


Reaction_has_mechanism
A boolean value indicating if the reaction has a mechanism in MARTS.


Mechanism_marts_ID
The MARTS ID of the mechanism.


Publication
The publication the reaction was taken from.




The next table describes the known mechanisms of terpene synthases. The mechanisms are divided into steps, which describe roughly the change of a single bond in the reactive carbocation. Steps are described by the types of reaction that are taking place. Every row is one step.




Column
Content




Enzyme_uniprot_ids
The UniProt IDs of enzymes that utilize this mechanism in their reaction, separated by commas.


Enzyme_genbank_ids
The GenBank IDs of the enzymes that utilize this mechanism in their reaction, separated by commas.


Enzyme_marts_ids
The MARTS IDs of the enzymes that utilize this mechanism in their reaction, separated by commas.


Substrate_smiles
The SMILES representation of the molecule that enters this reaction step. All diphosphates are written as oxoanions with charge on the diphosphate group.


Substrate_name
The commonly used name of the molecule that enters this step.


Substrate_marts_id
The MARTS ID of the molecule that enters this step.


Product_smiles
The SMILES representation of the product of this step. All diphosphates are written as oxoanions with charge on the diphosphate group.


Product_name
The commonly used name of the product of this step.


Product_marts_id
The MARTS ID of the product of this step.


Reaction_type
The type of this reaction step. Types are described in their section of the about page.


Evidence
The method of investigation for this mechanism. The methods are usually similarity, trivial, experiment, and calculation.


Publication
The publication the mechanism was taken from.


Mechanism_marts_id
The MARTS ID of the mechanism.