Protein Family Models

RHS proteins contain extended repeat regions. These repeats often appear to be involved in ligand binding (e.g. [1]). Note that this model may not find all the repeats in a protein and that it covers two RHS repeats. The 3D structure of an RHS-repeat-containing protein (the B and C components of an ABC toxin complex) has been determined. The RHS repeats form an extended strip of beta-sheet that spirals around to form a hollow shell, encapsulating the variable C-terminal domain [2]. [1]. 10341219. Teneurin-1, a vertebrate homologue of the Drosophila pair-rule gene ten-m, is a neuronal protein with a novel type of heparin-binding domain. Minet AD, Rubin BP, Tucker RP, Baumgartner S, Chiquet-Ehrismann R;. J Cell Sci 1999;112:2019-2032. [2]. 23913273. The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device. Busby JN, Panjikar S, Landsberg MJ, Hurst MR, Lott JS;. Nature. 2013;501:547-550. (from Pfam)

Date:

2024-10-29

This model represents a conserved unique core sequence shared by large numbers of proteins. It is occasional in the Archaea Methanosarcina barkeri) but common in bacteria and eukaryotes. Most fall into two large classes. One class consists of long proteins in which two classes of repeats are abundant: an FG-GAP repeat (PF01839) class, and an RHS repeat (PF05593) or YD repeat (TIGR01643). This class includes secreted bacterial insecticidal toxins and intercellular signalling proteins such as the teneurins in animals. The other class consists of uncharacterized proteins shorter than 400 amino acids, where this core domain of about 75 amino acids tends to occur in the N-terminal half. Over twenty such proteins are found in Pseudomonas putida alone; little sequence similarity or repeat structure is found among these proteins outside the region modeled by this domain.

Date:

2023-02-23

This HMM describes two tandem copies of a 21-residue extracellular repeat found in Gram-negative, Gram-positive, and animal proteins. The repeat is named for a YD dipeptide, the most strongly conserved motif of the repeat. These repeats appear in general to be involved in binding carbohydrate; the chicken teneurin-1 YD-repeat region has been shown to bind heparin.

Date:

2024-10-29