Information about enzyme mechanisms, the chemical reactions that occur in the active centres of enzymes, is scattered throughout the literature. These data may be difficult to consolidate, and in some cases, different mechanism proposals exist for the same enzyme. Difficulties arise from limitations in the experimental methods, which cannot follow enzyme reactions in real time. As a consequence, all the knowledge they produce about mechanisms is fragmentary. Examples include the identification of important residues by mutation, or snapshots of the structure with X-ray crystallography. Computational models, on the other hand, yield a complete picture of the mechanism including its energy profile, but the quality of these models is not homogeneous, and more accurate descriptions are still prohibitively time consuming. This state of affairs differs strikingly from protein sequence and structure, where central databases (Uniprot and PDB) exist, which ensure some level of consistency and data checks.<br/>MACiE (Mechanism, Annotation, and Classification in Enzymes) is a database of enzyme mechanisms that was created to fill this gap. Its purpose is twofold: to gather all the information about enzyme mechanisms in the same place so it can be consulted by the community; and to provide a dataset which can be used to understand enzyme function and evolution. Practical applications that could benefit from this data include the design of new enzymes and inhibitors.<br/>We are currently redesigning the MACiE database and website to make them more complete and easier to update and consult. MACiE now supports the inclusion of several mechanism proposals for the same enzyme, to reflect the rich literature. Tools for curators have been greatly improved. The creation and edition of new entries are now made entirely through the website, including the drawing of the 2D reaction schemes. Automation and data checks were added when applicable. The online tool allows for researchers outside the EBI to create new entries in the database, which can then be shown in the website. For people consulting the website, we are improving the search and browsing tools, and overhauling the interface to make it more user-friendly. In addition to the changes in the database and website, we are also carrying out a complete revision of existing MACiE entries, and merging CSA (Catalytic Site Atlas – A database of enzyme catalytic residues) entries into MACiE.

Redesign of MACiE: A database of enzyme mechanisms

254th National Meeting (2017)

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