Ubiquitin-binding domains - from structures to functions - PubMed (original) (raw)
Review
Ubiquitin-binding domains - from structures to functions
Ivan Dikic et al. Nat Rev Mol Cell Biol. 2009 Oct.
Abstract
Ubiquitin-binding domains (UBDs) are modular elements that bind non-covalently to the protein modifier ubiquitin. Recent atomic-level resolution structures of ubiquitin-UBD complexes have revealed some of the mechanisms that underlie the versatile functions of ubiquitin in vivo. The preferences of UBDs for ubiquitin chains of specific length and linkage are central to these functions. These preferences originate from multimeric interactions, whereby UBDs synergistically bind multiple ubiquitin molecules, and from contacts with regions that link ubiquitin molecules into a polymer. The sequence context of UBDs and the conformational changes that follow their binding to ubiquitin also contribute to ubiquitin signalling. These new structure-based insights provide strategies for controlling cellular processes by targeting ubiquitin-UBD interfaces.
Figures
Figure 1. Enzymatic cascade that leads to substrate ubiquitylation
The activity of three enzymes is required for ubiquitylation, an E1 activating enzyme, an E2 conjugating enzyme and an E3 ligating enzyme, which recognizes the substrate. The completion of one cycle results in a monoubiquitylated substrate. However, the cycle can be repeated to form polyubiquitylated substrates. Additional ubiquitin molecules can be ligated to a Lys residue (Lys6, Lys11, Lys27, Lys29, Lys33, Lys48 or Lys63) in a previously attached ubiquitin to form Lys-linked chains. Alternatively, ubiquitin molecules can be linked head-to-tail to form linear chains. Only homotypic chains are shown, however, some E2-E3 combinations produce chains of mixed linkage.
Figure 2. The ubiquitin–UBD network
A single type of molecule, ubiquitin, can be covalently attached to target proteins: as a single moiety (mono), as multiple single moieties (multiple), as chains coupled to the same lysine residue in ubiquitin (homotypic), mixed chains linked through different Lys residues in ubiquitin (branched) or head-to-tail bound ubiquitin moieties (linear). Specialized sets of ubiquitin-binding domains (UBDs) can read these post-translational modifications and mediate different outputs depending on the protein in which they are embedded. a | Two UBDs in the same protein can bridge two ubiquitylated targets. Alternatively, two proteins carrying oligomerization domains and UBDs can indirectly bridge the same ubiquitylated cargo. In all cases, this results in the formation of protein complexes, which might help to amplify a signal or activate a downstream activity. b | Specialized UBDs have also been discovered that are able to selectively discriminate between different types of ubiquitin chains. c | Lastly, the presence of two or more UBDs in a protein or the attachment of multiple ubiquitin moieties onto the same target can increase avidity and promote ubiquitin–UBD interactions despite their low affinity interactions. This phenomenon might be important to filter noise coming from non-specific transient ubiquitin–UBD interactions and to amplify only the output of proper ubiquitin–UBD pairs. UBDs that bind to one ubiquitin moiety are displayed as blue half moons, whereas those that interact specifically with the regions linking ubiquitin moieties are in orange. Double-sided UBDs are displayed as brown half moons. Arrows indicate protein–protein interactions.
Figure 3. Structural diversity contributes to the multiplicity of ubiquitin signalling
a | Ubiquitin contains a 5-stranded β-sheet, a 3.5-turn α-helix and a short 310 helix. Seven solvent-exposed Lys residues (displayed in blue) are available to assemble ubiquitin chains and the hydrophobic residues Leu8 (green), Ile44 (red) and Val70 (yellow) serve as a platform for many ubiquitin-binding domain (UBD) interactions. A ribbon representation of monoubiquitin is shown (PDB 1D3Z)b | Ubiquitin is a dynamic molecule in solution with conformational diversity. Distinct conformations are selected by individual UBDs. Several conformations adopted in solution are displayed to highlight ubiquitin's dynamic range of motions. Leu8, Ile44 and Val70 are shown in green, red and yellow, respectively. c | Ribbon representations of Lys48-linked diubiquitin (PDB 1AAR). d | Ribbon representations of Lys63-linked diubiquitin (PDB 2JF5). e | Ribbon representations of linear diubiquitin forming isopeptide bond between Met1 and Gly76 (PDB 2W9N) . Linkage of ubiquitin molecules into a polymer enhances structural diversity for robust signalling. The isopeptide bond linkage is shown in cyan in (c) and (d). Whereas Lys48-linked chains form compact structures due to inter-moiety interactions, Lys63-linked and linear ubiquitin chains are extended. In each case, the linker and its neighbouring region are chemically diverse.
Figure 4. Ubiquitin is recognized by structurally diverse domains
Several ubiquitin– ubiquitin-binding domain (UBD) complexes are displayed with ubiquitin (grey) in the same orientation to highlight the common use of its β-strand surface to bind diverse UBD structures. a | Ribbon representations of PLIC1 (Protein linking IAP with cytoskeleton 1) ] ubiquitin-associated (UBA) domain–ubiquitin (PDB 2JY6). b | Ribbon representations of ubiquitin-zinc finger domains of Rabex-5 A20 (PDB 2FIF), the NPL4 (nuclear protein localization 4) ZnF (NZF) domain (PDB 1Q5W) and isopeptidase T UBP (ubiquitin binding protein) (PDB 2G45) complexed with ubiquitin. c | Ribbon representations of ubiquitin in complex with the E2 ubiquitin-conjugating (Ubc) enzyme UBCH5c– (PDB 2FUH)d | GLUE (GRAM-like ubiquitin-binding in EAP45 domain–ubiquitin (PDB 2DX5;33). e | Ribbon representations of RPN13 (Regulatory Particle, Non-ATPase-like 13)– ubiquitin (1-150; PDB 2Z59). The 3-helix bundle structure of the UBA domain (a), E2 ubiquitin conjugating domain (c), and plekstrin homology (PH) domain (d, e) all bind to ubiquitin's Ile44-centred hydrophobic patch, but do so in diverse manners. These UBDs cannot simultaneously act upon a common monoubiquitin or ubiquitin moiety within a chain. Zinc finger domains are more diverse in their binding to ubiquitin; Npl4 NZF binds to the Ile44-centred surface whereas Rabex-5 A20 ZnF and the deubiquitinase (DUB; also known as deubiquitylating or deubiquitinating enzyme) isopeptidase T UBP bind to an Asp58-centred surface and the carboxyl terminus, respectively. In (b), the zinc atoms are displayed as red spheres, whereas in e), the sidechain atoms of His68 are displayed in yellow.
Figure 5. Multivalent interactions between ubiquitin and UBDs define chain specificity and increase affinity
a | HR23a ubiquitin-associated 2 (UBA2) domain (green) is sandwiched between the two ubiquitin moieties of Lys48-linked diubiquitin (grey) (PDB 1ZO6). This structure provides an explanation for this domain's preference for Lys48-linked chains, as the UBA domain contacts the ubiquitin linker region to significantly expand its binding surface beyond that possible for monoubiquitin. b | Structure of Lys63-linked diubiquitin bound to Rap80 (Receptor Associated Protein 80) illustrates why it binds to Lys63-, but not Lys48-linked chains (coordinates generously provided by Dr S. Fukai (University of Tokyo, Japan). Its contiguous helix binds simultaneously to two ubiquitin moieties, thereby increasing its affinity beyond that possible with monoubiquitin and defining the spacing between the two ubiquitin moieties to be greater than achievable with the Lys48 linkage. c | NF-κB essential modulator (NEMO) UBAN(ubiquitin binding in ABIN and NEMO) domain forms a coiled-coil, which binds two linear diubiquitins, . Extensive contacts are formed to both ubiquitin moieties thus conveying specificity for linear ubiquitin chains d | The structure of the single-helix double-sided HRS ubiquitin-interacting motif (UIM) bound to two ubiquitins reveals how it can target two ubiquitin molecules with equal affinity (PDB 2D3G). The ubiquitin molecules interact on opposite sides of this UIM and with a similar binding mode.
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