MEROPS: the peptidase database

The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
Nucleic Acids Research (Impact Factor: 9.11). 02/2008; 36(Database issue):D320-5. DOI: 10.1093/nar/gkm954
Source: PubMed


Peptidases (proteolytic enzymes or proteases), their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database ( aims to fulfil the need for an integrated source of information about these. The organizational principle of the database is a hierarchical classification in which homologous sets of peptidases and protein inhibitors are grouped into protein species, which are grouped into families and in turn grouped into clans. Important additions to the database include newly written, concise text annotations for peptidase clans and the small molecule inhibitors that are outside the scope of the standard classification; displays to show peptidase specificity compiled from our collection of known substrate cleavages; tables of peptidase-inhibitor interactions; and dynamically generated alignments of representatives of each protein species at the family level. New ways to compare peptidase and inhibitor complements between any two organisms whose genomes have been completely sequenced, or between different strains or subspecies of the same organism, have been devised.

Download full-text


Available from: Neil D Rawlings,
47 Reads
  • Source
    • "SPIs can be grouped into at least 74 different families depending on their sequence, topological and functional similarities [1] [9]. The pacifastin family is a newly identified SPIs family first discovered in 1987 from the haemolymph of the crayfish Pacifastacus leniusculus [10]. "
  • Source
    • "Protease inhibitors (PIs) are ubiquitous in all living organisms and it is divided into four classes based on their protease active site such as serine, cysteine, aspartic and metalloprotease . Until now, more than 16,000 PIs have been reported from various organisms; these PIs are categorized into 67 families ( [3]. Serine protease inhibitors (SPIs) play vital roles in many physiological functions including blood coagulation [4], inflammation [5], metamorphosis [6], complement system [7] and innate immune response. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Kazal-type serine protease inhibitor (KSPI) is a pancreatic secretary trypsin inhibitor which involves in various cellular component regulations including development and defense process. In this study, we have characterized a KSPI cDNA sequence of freshwater striped murrel fish Channa striatus (Cs) at molecular level. Cellular location analysis predicted that the CsKSPI was an extracellular protein. The domain analysis showed that the CsKSPI contains a Kazal domain at 47-103 along with its family signature between 61 and 83. Phylogenetically, CsKSPI is closely related to KSPI from Maylandia zebra and formed a sister group with mammals. The 2D structure of CsKSPI showed three α-helical regions which are connected with random coils, one helix at signal sequence and two at the Kazal domain region. The relative gene expression showed that the CsKSPI was highly expressed in gills and its expression was induced upon fungus (Aphanomyces invadans), bacteria (Aeromonas hydrophila) and poly I:C (a viral analogue) challenge. The CsKSPI recombinant protein was produced to characterize and study the CsKSPI gene specific functions. The recombinant CsKSPI strongly inhibited trypsin compared to other tested proteases. The results of the kinetic activity of CsKSPI against trypsin was Vmaxs = 1.62 nmole/min, KMs = 0.21 mM and Kis = 15.37 nM. Moreover, the recombinant CsKSPI inhibited the growth of Gram-negative bacteria A. hydrophila at 20 μM and Gram-positive bacteria Bacillus subtilis at the MIC50 of 15 μM. Overall, the study indicated that the CsKSPI was a potential trypsin inhibitor which involves in antimicrobial activity. Copyright © 2014. Published by Elsevier Ltd.
    Fish &amp Shellfish Immunology 11/2014; 42(2). DOI:10.1016/j.fsi.2014.11.027 · 2.67 Impact Factor
  • Source
    • "This gives insight into processes such as sub-functionalization, where gene families have expanded and then divided their functions between protein family members located in different parts of the cell. For example, bacterial genomes usually encode three Deg proteases, yeasts own one (occasionally duplicated), and four to five genes coding for Deg proteases are present in mammalian genomes (Kim and Kim, 2005; Rawlings et al., 2008; Huesgen et al., 2011). In plants, however, this family has expanded and plant genomes contain many more genes encoding Deg proteases. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Sub-functionalization during the expansion of gene families in eukaryotes has occurred in part through specific subcellular localization of different family members. To better understand this process in plants, compiled records of large-scale proteomic and fluorescent protein localization datasets can be explored and bioinformatic predictions for protein localization can be used to predict the gaps in experimental data. This process can be followed by targeted experiments to test predictions. The SUBA3 database is a free web-service at that helps users to explore reported experimental data and predictions concerning proteins encoded by gene families and to define the experiments required to locate these homologous sets of proteins. Here we show how SUBA3 can be used to explore the subcellular location of the Deg protease family of ATP-independent serine endopeptidases (Deg1-Deg16). Combined data integration and new experiments refined location information for Deg1 and Deg9, confirmed Deg2, Deg5, and Deg8 in plastids and Deg 15 in peroxisomes and provide substantial experimental evidence for mitochondrial localized Deg proteases. Two of these, Deg3 and Deg10, additionally localized to the plastid, revealing novel dual-targeted Deg proteases in the plastid and the mitochondrion. SUBA3 is continually updated to ensure that researchers can use the latest published data when planning the experimental steps remaining to localize gene family functions.
    Frontiers in Plant Science 08/2014; 5:396. DOI:10.3389/fpls.2014.00396 · 3.95 Impact Factor
Show more