MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases V2.0

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.Update 2.0: The accuracy of the data has been increased for the entire dataset, leading to deletion of multiple enzymes. Reorted product ratios has been recorded as well as expremental conditions. 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. Publication_doi DOI of the source publication Product_yield The reported ratio of the product, compare to other products at the same conditions. It is a text value. The existing formats are: X% meaning a relative percentage based usualy on the chromatogram (rarely exists as "less X%"), X where X is a number means a ratio compare to other products e.g. 2:1. Major, second, minor, trace, based on the definition in the publication. Second is the product that is close second to the major product. In some cases multiple products are marked as major. When mixed the order is: major > second > any number > minor > trace Major_substrate In some cases one of the accepted substrates is described as major, meaning that all others are accepted significantly less. Experiment_conditions Tags describing the reported conditions based on which the reaction was assigned to the enzyme. The tags are simplified abbreviations of methods used during the function elucidation. The methods of assigning the structure of the product are library - compariosn of MS spectra to a library or literature data, standard - comparison to an authentic standard. Negative_substrates Substrates that have been tested for this enzyme, but did not yield any product. 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.