The ring between ring fingers (RBR) protein family

Abstract

Proteins of the ring between ring fingers (RBR)-domain family are characterized by three groups of specifically clustered (typically eight) cysteine and histidine residues. Whereas the amino-terminal ring domain (N-RING) binds two zinc ions and folds into a classical cross-brace ring finger, the carboxy-terminal ring domain (C-RING) involves only one zinc ion. The three-dimensional structure of the central ring domain, the IBR domain, is still unsolved. About 400 genes coding for RBR proteins have been identified in the genomes of uni- and multicellular eukaryotes and some of their viruses, but the family has not been found in archaea or bacteria. The RBR proteins are classified into 15 major subfamilies (besides some orphan cases) by the phylogenetic relationships of the RBR segments and the conservation of their sequence architecture. The RBR domain mediates protein-protein interactions and a subset of RBR proteins has been shown to function as E3 ubiquitin ligases. RBR proteins have attracted interest because of their involvement in diseases such as parkinsonism, dementia with Lewy bodies, and Alzheimer's disease, and in susceptibility to some intracellular bacterial pathogens. Here, we present an overview of the RBR-domain containing proteins and their subcellular localization, additional domains, function, specificity, and regulation.

Figure 1

Multiple alignment of RBR domain segments. The figure includes the sequences of 64 representative RBR segments. This alignment is part of the grand alignment used to create the phylogenetic tree in Figure 2. The sequence identifier gives the subfamily code (first letter) followed by the taxon and the accession number in GenBank. The loop segments between the three ring-like domains are indicated by 'XX'. The gray bars at the bottom represent the degree of amino acid type conservation of alignment positions. The alignment was primarily generated with CLUSTALX [70] and edited manually. Taxon abbreviations: Am, Apis mellifera; At, Arabidopsis thaliana; Ce, Caenorhabditis elegans; Dd, Dictyostelium discoideum; Dm, Drosophila melanogaster; Dr, Danio rerio; Gz, Gibberella zeae; Hs, Homo sapiens; Nc, Neurospora crassa; Sp, Schizosaccharomyces pombe.

Figure 2

Phylogenetic tree of RBR domain segments. A grand alignment of RBR segments from 102 proteins representative of the most populated subgroups was used to create the tree. We used the program SEAVIEW and the tool ATV from the Forester package [71-73]. Each entry is labeled as in Figure 1. Typically, subfamily members cluster nicely together and the phylogenetic relationships within subfamilies are determined with significance. Closer to the root of the tree, the branching becomes increasingly uncertain. Some groups of fungal and protozoan sequences are more heterogeneous and appear at several tree positions. The D. discoideum sequence XP_646567.1 does not appear together with other ARA54 sequences but was assigned to the group 'B (ARA54)' because of the RWD domain in the sequence architecture.

Figure 3

Structures of ring domains in the RBR segments. The structure graphics were generated with the program VMD [74]. The backbone trace and the secondary structure are shown as ribbons and the zinc ions as red spheres. (a) Carboxy-terminal part of the RBR region (C-RING) in the human Ariadne-1 homolog protein HHARI (PDB accession number 1WD2; residues 326-395 of UNIPROT accession number Q9Y4X5; subfamily A1/Ari1). (b) The N-RING of the RBR segment of the human UbcM4-interacting protein 4 (PDB accession number 1WIM; residues 20-100 of UNIPROT accession number P50876; subfamily C/RNF144).

Figure 4

Sequence architecture of RBR proteins. The detailed sequence architecture of the subfamilies of RBR proteins is shown. The globular domains (such as cullin) and non-globular regions (negative-charge clusters or proline-rich regions) are color-coded as shown in the key. It should be noted that the typical sequence architecture is shown. There are several exceptions: for example, PAUL proteins mostly contain three additional zinc fingers, but a few representatives have only one. Similarly, dorfins have two predicted hydrophobic helices with the exception of the protozoan members, which have only one or none. The two sequences of the Fungi1 group are very diverse and have only the RBR segment in common. Among the Plant1 representatives, one protein contains two RRM domains instead of the usual two KH domains. Domain accession numbers: APC10, PF03256; cullin, SM00182; DEXDc, SM00487; IBR, SM00647; RWD, SM00591; DUF1605, PF07717; HA2, PF04408; HELICc, SM00490; KH, SM00322; RRM, SM 00360; ANK, SM002481; UBA, SM00165; UBQ, SM00213; UIM, SM00726; and ZnF_RBZ, SM00547. The first two letters 'PF' and 'SM' indicate the PFAM and SMART databases, respectively.

Figure 5

Known interactors with the RBR protein. The interacting proteins for each region are boxed and are preceded by the name of the subfamily of RBR proteins with which they interact: A, Ariadne; A3, Parc; B, ARA54; D, dorfin; P, parkin; C, RNF144; X, XAP; U, Paul; T, TRIAD3. The additional amino-terminal domains present in some subfamilies of RBR proteins are highlighted in light blue and indicated by the domain abbreviation with the subfamily in which they are found in parentheses. UBL, ubiquitin-like domain; UBA, ubiquitin-associated domain; ZnF_RBZ, zinc finger; cullin, cullin-like domain; ARM/HEAT, Armadillo and HEAT repeats; APC10, anaphase-promoting complex subunit 10. A carboxy-terminal hydrophobic segment is present in the dorfins. Additional substrates and interactors are listed in Additional data file 1.