Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2015 Jul 17:10:36.
doi: 10.1186/s13062-015-0066-5.

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

Gurmeet Kaur  1 , Srikrishna Subramanian  2
Affiliations

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

Gurmeet Kaur et al. Biol Direct. .

Abstract

Background: The N-end rule pathway is a part of the ubiquitin-dependent proteolytic system wherein N-recognin proteins recognize the amino terminal degradation signals (N-degrons) of the substrate. The type 1 N-degron recognizing UBR-box domain of the eukaryotic Arg/N-end rule pathway is known to possess a novel three-zinc-stabilized heart-shaped fold.

Results: Using sequence and structure analysis we argue that the UBR-box fold emerged from a binuclear RING-like treble clef zinc finger. The RING-like core is preserved in the UBR-box and the metal-chelating motifs display significant sequence and structural similarity to B-box and ZZ domains. UBR-box domains retrieved in our analysis co-occur with a variety of other protein domains, suggestive of its involvement in diverse biological roles. The UBR-box is a unique family of RING-like treble clefs as it displays a distinct circular permutation at the zinc-knuckle of the first zinc-binding site unlike other documented permutations of the RING-like domains which occur at the second zinc-binding site. The circular permutation of the RING-like treble clef scaffold has possibly aided the gain of a novel and relatively deep cleft suited for binding N-degrons. The N- and C-terminal extensions to the circularly permuted RING-like region bind a third zinc ion, which likely provides additional stability to the domain by keeping the two halves of the permuted zinc-knuckle together.

Conclusions: Structural modifications and extensions to the RING-like core have resulted in a novel UBR-box fold, which can recognize and target the type 1 N-degron containing proteins for ubiquitin-mediated proteolysis. The UBR-box appears to have emerged during the expansion of ubiquitin system pathway-related functions in eukaryotes, but is also likely to have other non-N-recognin functions as well.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1
Structure of the UBR-box (a) UBR-box from human UBR1 (PDB identifier 3NY1_A) (b) UBR-box from S. cerevisiae UBR1 (PDB identifier 3NIH_A). The structures have been colored from the N- to C-terminal in a gradient of blue to red. The zinc-chelating residue which displays circular permutation in S. cerevisiae UBR-box with respect to the human UBR-box is marked with a dotted circle. The shared metal-chelating residue is indicated by a red arrow
Fig. 2
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
Fig. 3
Fig. 3
Structure based multiple sequence alignment of B-box, ZZ domain and UBR-box. PDB/UniProt identifier, start and end aminoacid numbers are indicated for each sequence. Identifiers of the representative sequences of the B-box are highlighted in peach, ZZ domain in light green and UBR-box in light blue. Secondary structure diagram is depicted above the alignment. The zinc-binding residues (Cys/His) of the first zinc binding site of the binuclear treble clef have been highlighted in black, those of the second zinc binding site in grey, those of the third zinc binding site (for the UBR-box) in dark blue and other aminoacids at equivalent position in red. Residues that may potentially serve as metal-chelating ligands are highlighted in pink. The shared ligand in the UBR-box is indicated by an asterisk (*) and highlighted in black and blue. The sequence region in between the circularly permuted zinc-knuckle of the UBR-box, which is not present in the B-box and the ZZ domain, is shown in a separate box under the alignment of the common binuclear RING-like regions. Regions of circular permutation are separated by a small blue colored box and sequence numbers of the regions around the circular permutation are colored in red. Regions where the structures are not superimposable are shown in italics. Small aminoacids (Gly, Pro) in the vicinity of the zinc-binding ligands are colored red. Uncharged residues (all aminoacids except Asp, Glu, Lys and Arg) in mostly hydrophobic sites are highlighted yellow. Long insertions are not shown and the number of omitted residues is boxed in green
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Varshavsky A. The N-end rule pathway and regulation by proteolysis. Protein Sci. 2011 - PMC - PubMed
    1. Tasaki T, Sriram SM, Park KS, Kwon YT. The N-end rule pathway. Annu Rev Biochem. 2012;81:261–89. doi: 10.1146/annurev-biochem-051710-093308. - DOI - PMC - PubMed
    1. Tasaki T, Mulder LC, Iwamatsu A, Lee MJ, Davydov IV, Varshavsky A, et al. A family of mammalian E3 ubiquitin ligases that contain the UBR box motif and recognize N-degrons. Mol Cell Biol. 2005;25(16):7120–36. doi: 10.1128/MCB.25.16.7120-7136.2005. - DOI - PMC - PubMed
    1. Matta-Camacho E, Kozlov G, Li FF, Gehring K. Structural basis of substrate recognition and specificity in the N-end rule pathway. Nat Struct Mol Biol. 2010;17(10):1182–7. doi: 10.1038/nsmb.1894. - DOI - PubMed
    1. Choi WS, Jeong BC, Joo YJ, Lee MR, Kim J, Eck MJ, et al. Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Mol Biol. 2010;17(10):1175–81. doi: 10.1038/nsmb.1907. - DOI - PubMed

Publication types

MeSH terms

Substances

LinkOut - more resources