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.

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Available from: Neil D Rawlings
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    • "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]. "

    Full-text · Dataset · Aug 2015
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    • "BRENDA (Chang, Scheer, Grote, Schomburg, & Schomburg, 2009) at using the MEROPS database (Rawlings & Barrett, 1999;Rawlings, Morton, Kok, Kong, & Barrett, 2008) at The cleavage specificity of the thermolysin enzyme was analysed using peptide cutter and the BIOPEP database (Minkiewicz, Dziuba, Iwaniak, Dziuba, & Darewicz, 2008) at "
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    ABSTRACT: The generation of the antimicrobial peptide caseicin A (IKHQGLPQE) from a casein substrate using proteolytic enzymes was assessed in silico. This bioinformatic analysis predicted that thermolysin (EC and thermolysin-like enzymes (EC are likely candidates to liberate the bioactive peptide from αS1-casein. Commercially available sources of the thermolysin enzyme from industrial suppliers were subsequently shown to liberate the 1049 Da caseicin A peptide, under various conditions of hydrolysis, at both lab and pilot scale. The antimicrobial ability of the hydrolysates to reduce pathogen numbers spiked in infant formula trials was subsequently confirmed. For example, numbers of Cronobacter sakazakii were reduced 1000 fold after 3 h of incubation at 37 °C. In conclusion, this study demonstrates the potential to improve the safety of infant milk formula using milk-derived bioactive peptides.
    Full-text · Article · Apr 2015 · International Dairy Journal
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    • "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. "
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    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.
    Full-text · Article · Nov 2014 · Fish & Shellfish Immunology
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