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. 2019 Jan 1:2019:baz103.
doi: 10.1093/database/baz103.

ProtMiscuity: a database of promiscuous proteins

Ana Julia Velez Rueda  1 , Nicolas Palopoli  1 , Matías Zacarías  1 , Leandro Matías Sommese  1 , Gustavo Parisi  1
Affiliations

ProtMiscuity: a database of promiscuous proteins

Ana Julia Velez Rueda et al. Database (Oxford). .

Abstract

Promiscuous behaviour in proteins and enzymes remains a challenging feature to understand the structure-function relationship. Here we present ProtMiscuity, a manually curated online database of proteins showing catalytic promiscuity. ProtMiscuity contains information about canonical and promiscuous activities comprising 88 different reactions in 57 proteins from 40 different organisms. It can be searched or browsed by protein names, organisms and descriptions of canonical and promiscuous reactions. Entries provide information on reaction substrates, products and kinetic parameters, mapping of active sites to sequence and structure and links to external resources with biological and functional annotations. ProtMiscuity could assist in studying the underlying mechanisms of promiscuous reactions by offering a unique and curated collection of experimentally derived data that is otherwise hard to find, retrieve and validate from literature.

Keywords: database; promiscuity; proteins.

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Figures

Figure 1
Figure 1
(A) Homepage of ProtMiscuity. The database can be searched using protein names, organism and target reaction. In this example, a search for the protein alpha-amylase is performed. (B) Results page. It shows all matches to the query term in the form of protein-specific cards. In this example, alpha-amylases from two distinct organisms are retrieved. (C) Information page. Clicking on one protein’s card displays all the available information about it, organized in five sections of interest. From top to bottom, left to right: a general description of the protein; the mapping of the canonic and promiscuous active sites, along with other sources of relevant information, on the protein’s sequence; information about canonic and promiscuous activities, with known substrates, products and kinetic parameters (top panel); a visualization of each available structure of the protein, with catalytic sites mapped on it; and examples of conformational diversity, plus links to relevant bibliography and other databases, as separate tabs (bottom panel).
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