The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database

By Neil D. Rawlings, Alan J. Barrett, Paul D. Thomas, Xiaosong Huang, Alex Bateman, Robert D. Finn. 2017

1,458 citations recorded by the source corpus.

Abstract The MEROPS database (http://www.ebi.ac.uk/merops/) is an integrated source of information about peptidases, their substrates and inhibitors. The hierarchical classification is: protein-species, family, clan, with an identifier at each level. The MEROPS website moved to the EMBL-EBI in 2017, requiring refactoring of the code-base and services provided. The interface to sequence searching has changed and the MEROPS protein sequence libraries can be searched at the EMBL-EBI with HMMER, FastA and BLASTP. Cross-references have been established between MEROPS and the PANTHER database at both the family and protein-species level, which will help to improve curation and coverage between the resources. Because of the increasing size of the MEROPS sequence collection, in future only sequences of characterized proteins, and from completely sequenced genomes of organisms of evolutionary, medical or commercial significance will be added. As an example, peptidase homologues in four proteomes from the Asgard superphylum of Archaea have been identified and compared to other archaean, bacterial and eukaryote proteomes. This has given insights into the origins and evolution of peptidase families, including an expansion in the number of proteasome components in Asgard archaeotes and as organisms increase in complexity. Novel structures for proteasome complexes in archaea are postulated.

Subfields: Molecular Biology, Oncology

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Citations in the corpus

The Pfam protein families database in 2019 (2018, background): “Of these, carboxypeptidase A1 favours substrate residues in the cleavage site with aromatic or branched side chains, while carboxypeptidase E favours basic amino acids (7).”
HMMER web server: 2018 update (2018, methodology): “We have also added the sequences from the MEROPS (15) database of proteolytic enzymes, which allows the precise annotation of peptidase subunits on query sequences by querying against the MEROPS holotype sequence database.”
The EMBL-EBI search and sequence analysis tools APIs in 2019 (2019, methodology): “These include MEROPS (24) databases, ChEMBL (25) targets, UniProtKB Reference Proteomes (8), as well as protein family databases used by HMMER3 (4).”
Insights into Plant Interactions and the Biogeochemical Role of the Globally Widespread Acidobacteriota Phylum (2023, methodology): “Peptidases were searched against MEROPS ‘pepunit’ database (Rawlings et al., 2018) also implemented in METABOLIC.”
Pfam: The protein families database in 2021 (2020, background): “The other protease activity in these viruses is described in Pfam:PF05409 usually known as Main protease (M-pro domain) or 3C-like proteinase (3CL-pro), corresponding to NSP5, a member of MEROPS (15) peptidase family C30.”
BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities (2019, background): “Example information about a single enzyme (plasmin; EC 3.4.21.7; MEROPS ID: S01.”
PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools (2018, background): “As a first example, published last year (19), we have worked with the MEROPS database of peptidases (proteases) and peptidase inhibitors.”