BRENDA in 2019: a European ELIXIR core data resource

Abstract

The BRENDA enzyme database (www.brenda-enzymes.org), recently appointed ELIXIR Core Data Resource, is the main enzyme and enzyme-ligand information system. The core database provides a comprehensive overview on enzymes. A collection of 4.3 million data for ∼84 000 enzymes manually evaluated and extracted from ∼140 000 primary literature references is combined with information obtained by text and data mining, data integration and prediction algorithms. Supplements comprise disease-related data, protein sequences, 3D structures, predicted enzyme locations and genome annotations. Major developments are a revised ligand summary page and the structure search now including a similarity and isomer search. BKMS-react, an integrated database containing known enzyme-catalyzed reactions, is supplemented with further reactions and improved access to pathway connections. In addition to existing enzyme word maps with graphical information of enzyme specific terms, plant word maps have been developed. They show a graphical overview of terms, e.g. enzyme or plant pathogen information, connected to specific plants. An organism summary page showing all relevant information, e.g. taxonomy and synonyms linked to enzyme data, was implemented. Based on a decision by the IUBMB enzyme task force the enzyme class EC 7 has been established for 'translocases', enzymes that catalyze a transport of ions or metabolites across cellular membranes.

Figure 1.

(A) The ligand summary page of acetylcholinesterase inhibitor tacrine containing the inhibitor table linked with enzyme 3D structures. The user can click at the (+)-icon to show the specific data of the EC number 3.1.1.7 or click at the (−)-icon to hide it. (B) 3D-structure search result page of acetylcholinesterase accessible via the entry page using the ‘Classic View’. (C) 3D enzyme structure of acetylcholinesterase in combination with tacrine.

Figure 2.

A similarity search for known proton-pump inhibitors with the parent structure.

Figure 3.

Distribution of unique reactions between BRENDA, KEGG, MetaCyc and SABIO-RK, not shown are the number of common reactions of BRENDA/KEGG and MetaCyc/SABIO-RK.

Figure 4.

A reaction specific pathway view of the vitamin E metabolism in BKMS-react.

Figure 5.

Organism summary page of Glycine max.