KNOTTIN: the knottin or inhibitor cystine knot scaffold in 2007

Abstract

The KNOTTIN database provides standardized information on the small disulfide-rich proteins with a knotted topology called knottins or inhibitor cystine knots. Static pages present the essential historical or recent results about knottin discoveries, sequences, structures, syntheses, folding, functions, applications and bibliography. New tools, KNOTER3D and KNOTER1D, are provided to determine or predict if a user query (3D structure or sequence) is a knottin. These tools are now used to automate the database update. All knottin structures and sequences in the database are now standardized according to the knottin nomenclature based on loop lengths between knotted cysteines, and to the knottin numbering scheme. Therefore, the whole KNOTTIN database (sequences and structures) can now be searched using loop lengths, in addition to keyword and sequence (BLAST, HMMER) searches. Renumbered and structurally fitted knottin PDB files are available for download as well as renumbered sequences, sequence alignments and logos. The knottin numbering scheme is used for automatic drawing of standardized two-dimensional Colliers de Perles of any knottin structure or sequence in the database or provided by the user. The KNOTTIN database is available at http://knottin.cbs.cnrs.fr.

Spider toxins comprising disulfide‐rich and linear amphipathic domains: a new class of molecules identified in the lynx spider Oxyopes takobius

“…X m+4 C 9 in our case), which is found in numerous peptides [27,28]. We conclude that, in OtTx, as well as in OxyTx, the three core ICK disulfides (C ; the latter is in fact part of the ESM and is found in most spider toxins containing eight cysteine residues).…”

Discovery of Linear Cyclotides in Monocot Plant Panicum laxum of Poaceae Family Provides New Insights into Evolution and Distribution of Cyclotides in Plants

“…Although there is little sequence homology of cyclotide precursors in different plant families, cyclotides of the Poaceae, Rubiaceae, Violaceae, and Fabaceae were all found to preserve the cystine knot arrangement, suggesting its structural and functional importance. The cystine knot arrangement is found in a variety of unrelated protein families of diverse species such as fungi, cone snails, snake venoms, insects, spiders, and plants (42). In plants, cystine knot peptides with molecular mass Ͻ4 kDa are known to be stable to heat and enzymatic degradation, and the cystine knot arrangement is considered to be a major contributing factor (3).…”

The Toxicogenomic Multiverse: Convergent Recruitment of Proteins Into Animal Venoms

“…The vast majority of these toxins contain the inhibitory cysteine knot (ICK) motif (also known as the knottin fold) that directs their three-dimensional fold (62,120). Structurally similar peptides are also present in other arthropods and plants, where they function as either toxins targeting Ca 2+ channels (scorpion and assassin bug toxins), antimicrobial agents (horseshoe crab tachystatin and plant thionins), or protease inhibitors (plant cyclotides).…”