CutDB: a proteolytic event database

Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2007; 35(Database issue):D546-9. DOI: 10.1093/nar/gkl813
Source: PubMed

ABSTRACT Beyond the well-known role of proteolytic machinery in protein degradation and turnover, many specialized proteases play a key role in various regulatory processes. Thousands of highly specific proteolytic events are associated with normal and pathological conditions, including bacterial and viral infections. However, the information about individual proteolytic events is dispersed over multiple publications and is not easily available for large-scale analysis. CutDB is one of the first systematic efforts to build an easily accessible collection of documented proteolytic events for natural proteins in vivo or in vitro. A CutDB entry is defined by a unique combination of these three attributes: protease, protein substrate and cleavage site. Currently, CutDB integrates 3070 proteolytic events for 470 different proteases captured from public archives (such as MEROPS and HPRD) and publications. CutDB supports various types of data searches and displays, including clickable network diagrams. Most importantly, CutDB is a community annotation resource based on a Wikipedia approach, providing a convenient user interface to input new data online. A recent contribution of 568 proteolytic events by several experts in the field of matrix metallopeptidases suggests that this approach will significantly accelerate the development of CutDB content. CutDB is publicly available at

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Available from: Alexey M Eroshkin, Aug 21, 2015
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    • "The main component of Proteasix is the underlying cleavage site database (CS database). The CS database has been built using information on human proteases from CutDB [13], Uniprot and the literature, collected through both manual literature mining and automated Java scripts. Each protease was associated with their corresponding CS sequences in their longest form (i.e. "
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    • "MMPs in primary explant collective cell migration T. M. McDonald et al. site comparisons were performed using CutDB (Igarashi et al., 2007) to identify cleavage sites in pro-MMPs and conservation between human and zebrafish sites determined using the alignments generated by BLAST. "
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    ABSTRACT: Zebrafish keratocytes collectively migrate rapidly when established in explant cultures but little is known about the signals that initiate motility or the signal transduction pathways that result in an epithelial to mesenchymal transition. Matrix metalloproteinases (MMPs) are strong candidates for playing a role in this regulation and have previously not been analysed in this wound healing model system. Results presented here document a rapid and dramatic rise in MMP14a, MMP2, MMP9 and MMP13a mRNA levels over time. In a motility assay, a broad-spectrum MMP inhibitor and an inhibitor specific for MMP2 and MMP9 significantly decrease cell migration in a dose dependent manner but treatment with an MMP13 specific inhibitor significantly increases cell sheet area. Immunofluorescence staining with an antibody specific for the catalytic domain of MMP14 indicates that activated MMP14 protein is highly expressed on cells at the leading edge of a sheet compared with follower cells in the centre of the sheet, and is augmented further in leader cells that are stretched, thus likely in the process of detaching from the cell sheet. These data are consistent with a model in which active MMP14 at the leading edge of cell sheets in explant cultures triggers activation of MMP2 and/or MMP9, thus creating promigratory signal(s) that outweigh the inhibitory role of targets cleaved by MMP13. Taken together, these data suggest that MMPs play an important but complex role in regulating the collective cell migration of zebrafish keratocytes and provide support for the relevance of using zebrafish as a model for human disease.
    12/2013; 20(2). DOI:10.1002/cbi3.10006
  • Osterreichische Krankenpflegezeitschrift 02/1980; 33(1):5-14.
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