Protein Family Models

This putative domain is found in a range of RHS proteins. (from Pfam)

Date:

2024-08-14

WHH is a predicted nuclease of the HNH/ENDO VII superfamily of the treble clef fold. The name is derived from the conserved motif WHH. It is found in bacterial polymorphic toxin systems [1] and functions as a toxin module. WHH is the shortest version of HNH nuclease families. Like AHH and LHH, the WHH nuclease contains 4 conserved histidines of which the first one is predicted to bind a metal-ion and other three ones are involved in activation of water molecule for hydrolysis [1]. [1]. 21306995. A novel immunity system for bacterial nucleic acid degrading toxins and its recruitment in various eukaryotic and DNA viral systems. Zhang D, Iyer LM, Aravind L;. Nucleic Acids Res. 2011;39:4532-4552. (from Pfam)

Date:

2024-10-16

Colicin-like bacteriocins are complex structures with an N-terminal beta-barrel translocation domain (Pfam:PF09000), a long double-alpha-helical receptor-binding domain (Pfam:PF11570) and this C-terminal RNAse/DNase domain with endonuclease activity. Their competitor bacteriocidal action is by a process that involves binding to a surface receptor, entering the cell, and, finally, killing it. The lethal action of colicin E3 is a specific cleavage in the ribosomal decoding A site. The crystal structure of colicin E3 reveals a Y-shaped molecule with the receptor binding domain forming a 100 Angstrom long stalk and the two globular heads of the translocation domain and this catalytic domain comprising the two arms [2]. [1]. 10368275. The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS;. Structure. 1999;7:91-102. [2]. 11741540. Crystal structure of colicin E3: implications for cell entry and ribosome inactivation. Soelaiman S, Jakes K, Wu N, Li C, Shoham M;. Mol Cell. 2001;8:1053-1062. (from Pfam)

Date:

2024-10-16

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

Date:

2024-08-14

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