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Fig. 2 | Biology Direct

Fig. 2

From: The UBR-box and its relationship to binuclear RING-like treble clef zinc fingers

Fig. 2

Comparison of the UBR-box with binuclear RING-like treble clef domains (a) Arrangement of secondary structure elements in mononuclear treble clef, binuclear RING-like treble clef, zinc ribbon domains and the circularly permuted RING-like core of the UBR-box fold. The position of zinc ligands is indicated by diamonds. The most commonly observed metal-chelating aminoacids in the respective domains as per Pfam consensus are shown in blue above the diamonds. For the RING-like binuclear treble clef, the zinc-binding motif of the classical RING family is depicted. However, the motif is variable among different RING-like treble clefs, for example, in the B-box and ZZ domain, the commonly observed metal-chelating motif is CC/HCCCCHH and CCCCCCHH, respectively. The zinc ions have been numbered as per their standard reference for treble clef folds [8, 10]. The zinc ion of the treble clef is numbered ‘1’, the second zinc ion seen in binuclear treble clefs is numbered ‘2’ and the third zinc ion of the UBR-box is numbered ‘3’. β-strands are represented as arrows and α-helices are shown as rectangles/cylinders. The secondary structure elements of mononuclear treble clef have been colored as follows: zinc-knuckle in red, zinc-knuckle containing β-hairpin in purple, primary β-hairpin in yellow and α-helix in cyan. In the binuclear RING-like treble clefs, an additional β-strand is present at the C-terminal which is colored grey. For the rubredoxin-like zinc ribbon region, the primary β-hairpin is colored purple, the secondary β-hairpin in yellow and the zinc-knuckles in red. As indicated, the first and second zinc-binding sites of the RING-like domain structurally resemble a classical mononuclear treble clef and a rubredoxin-like zinc ribbon domain, respectively. (b) RING finger domain from E3 ubiquitin-protein ligase Hakai (PDB identifier 3VK6_A) (c) B-box from E3 ubiquitin-protein ligase TRIM63 (PDB identifier 3DDT_A) (d) ZZ domain from zinc finger SWIM domain-containing protein 2 (PDB identifier 2DIP_A) (e) Binuclear RING-like region of the UBR-box (PDB identifier 3NY1_A) (f) The full length UBR-box (PDB identifier 3NY1_A) with extensions to the RING-like core, which ligate the third zinc ion, colored in white. The RING-like core scaffold in panels (b-f) has been colored similarly. Zinc ions are shown as orange spheres and side chains of zinc-chelating aminoacids are represented as sticks

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