title: Comparison of protein repeat classifications based on structure and sequence families.
abstract: Tandem repeats (TR) in proteins are common in nature and have several unique functions. They come in various forms that are frequently difficult to recognize from a sequence. A previously proposed structural classification has been recently implemented in the RepeatsDB database. This defines five main classes, mainly based on repeat unit length, with subclasses representing specific folds. Sequence-based classifications, such as Pfam, provide an alternative classification based on evolutionarily conserved repeat families. Here, we discuss a detailed comparison between the structural classes in RepeatsDB and the corresponding Pfam repeat families and clans. Most instances are found to map one-to-one between structure and sequence. Some notable exceptions such as leucine-rich repeats (LRRs) and α-solenoids are discussed.
authors.affiliation: Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35121 Padova, Italy.
authors.forename: Lisanna
authors.initials: L
authors.lastname: Paladin
authors.affiliation: Department of Biomedical Sciences, University of Padua, viale G. Colombo 3, 35121 Padova, Italy silvio.tosatto@unipd.it.
authors.forename: Silvio C E
authors.initials: SC
authors.lastname: Tosatto
mesh_terms: D000818:Animals; D017124:Conserved Sequence; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D040901:Proteomics / Q000379:methods*; D020449:Repetitive Sequences, Amino Acid; D020080:Tandem Repeat Sequences
keywords: Pfam; RepeatsDB; functional classification; structural classification; tandem repeat proteins