MEROPS: the peptidase database
Reads0
Chats0
TLDR
The MEROPS database has added an analysis tool to the relevant species pages to show significant gains and losses of peptidase genes relative to related species, and has collected over 39 000 known cleavage sites in proteins, peptides and synthetic substrates.Abstract:
Peptidases (proteolytic enzymes) are of great relevance to biology, medicine and biotechnology. This practical importance creates a need for an integrated source of information about them, and also about their natural inhibitors. The MEROPS database (http://merops.sanger.ac.uk) aims to fill this need. The organizational principle of the database is a hierarchical classification in which homologous sets of the proteins of interest are grouped in families and the homologous families are grouped in clans. Each peptidase, family and clan has a unique identifier. The database has recently been expanded to include the protein inhibitors of peptidases, and these are classified in much the same way as the peptidases. Forms of information recently added include new links to other databases, summary alignments for peptidase clans, displays to show the distribution of peptidases and inhibitors among organisms, substrate cleavage sites and indexes for expressed sequence tag libraries containing peptidases. A new way of making hyperlinks to the database has been devised and a BlastP search of our library of peptidase and inhibitor sequences has been added.read more
Citations
More filters
Journal ArticleDOI
Mapping protease substrates by using a biotinylated phage substrate library.
Michael D. Scholle,Ushma Kriplani,Amanda Pabon,Kamakshi Sishtla,Marc J. Glucksman,Brian K. Kay +5 more
TL;DR: A bacteriophage M13 substrate library encoding the AviTag (BirA substrate) and combinatorial heptamer peptides displayed at the N terminus of the mature form of capsid protein III is described and used to map the specificity of human Factor Xa and a neuropeptidase, neurolysin.
Journal ArticleDOI
Atomic-resolution crystal structure of the proteolytic domain of Archaeoglobus fulgidus lon reveals the conformational variability in the active sites of lon proteases.
Istvan Botos,E.E. Melnikov,Scott Cherry,Serguei Kozlov,O.V. Makhovskaya,Joseph E. Tropea,Alla Gustchina,T. V. Rotanova,Alexander Wlodawer +8 more
TL;DR: It is established that full-length wtAfLonB is proteolytically active in an ATP-dependent manner and raised the possibility that, although isolated proteolytic domains of both AfLon B and E.coli LonA are able to assemble into expected functional hexamers, the presence of the other domains, as well as substrate binding, may be needed to stabilize the productive conformation of their active sites.
Journal ArticleDOI
Overexpression of MpCYS4, A Phytocystatin Gene from Malus prunifolia (Willd.) Borkh., Enhances Stomatal Closure to Confer Drought Tolerance in Transgenic Arabidopsis and Apple
TL;DR: It is demonstrated that MpCYS4 is involved in ABA-mediated stress signal transduction and confers drought tolerance at least in part by enhancing stomatal closure and up-regulating the transcriptional levels of A BA- and drought-related genes.
Journal ArticleDOI
Opportunities for structure-based design of protease-directed drugs.
TL;DR: The development of drugs such as aliskiren and tipranavir, which inhibit renin and HIV protease, respectively, testifies to the success of the experimental structure determination approach.
Journal ArticleDOI
RASMOT-3D PRO: a 3D motif search webserver
TL;DR: This paper describes here the RASMOT-3D PRO webserver that performs a systematic search in 3D structures of protein for a set of residues exhibiting a particular topology and provides an interactive list of identified protein structures exhibiting residues of similar topology as the motif searched.
References
More filters
Journal ArticleDOI
Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Book
Molecular Evolutionary Genetics
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Journal ArticleDOI
Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features
Wolfgang Kabsch,Chris Sander +1 more
TL;DR: A set of simple and physically motivated criteria for secondary structure, programmed as a pattern‐recognition process of hydrogen‐bonded and geometrical features extracted from x‐ray coordinates is developed.
Journal ArticleDOI
The Pfam protein families database
Marco Punta,Penny Coggill,Ruth Y. Eberhardt,Jaina Mistry,John Tate,Chris Boursnell,Ningze Pang,Kristoffer Forslund,Goran Ceric,Jody Clements,Andreas Heger,Liisa Holm,Erik L. L. Sonnhammer,Sean R. Eddy,Alex Bateman,Robert D. Finn +15 more
TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.