NUB1 is an adaptor protein which negatively regulates the ubiquitin-like protein Nedd8 as well as neddylated proteins levels through proteasomal degradation [, ]. It has been shown to be regulated by Mdm2 (E3 ubiquitin ligase) through ubiquitination on its lysine 159 [].
This entry includes N-terminal ubiquitin-like domain from proteins such as NEDD8 ultimate buster 1.NUB1 is an adaptor protein which negatively regulates the ubiquitin-like protein Nedd8 as well as neddylated proteins levels through proteasomal degradation [, ]. It has been shown to be regulated by Mdm2 (E3 ubiquitin ligase) through ubiquitination on its lysine 159 [].
This entry represents a group of proteases from bacteria, invertebrates, fungi and plants, including Nep1/2 from Schizosaccharomyces pombe. Nep1/2 are deneddylating enzymes that process full-length nedd8 to its mature form and deconjugate nedd8 from targeted proteins [].
This entry represents a presumed C-terminal domain of ubiquitin 3 binding proteins (But2). But2 is conserved in yeasts. It binds to Uba3 and is involved in the NEDD8 signalling pathway [].
This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue [].
Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin []. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis []. This entry also includes Nedd8-like proteins from fungi and plants.
APP-BP1 (beta-Amyloid precursor protein binding protein 1), also known as Ula1 in yeasts, is a regulatory subunit of the E1 enzyme. Human APP-BP1 is necessary for cell cycle progression through the S-M checkpoint []. Drosophila APP-BP1 interacts antagonistically with APPL (APP-like protein) during Drosophila development [].Ubiquitin-like proteins (ublps) are conjugated to their targets by the sequential action of E1, E2 and often E3 enzymes. Each Ublp has a dedicated E1, or activating enzyme, that initiates its conjugation cascade. In humans the NEDD8 activating E1 enzyme is a heterodimer composed of APP-BP1 and UBA3 subunits. The ubiquitin-like protein (Ublp) NEDD8 regulates cell division, signalling and embryogenesis [].
E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains [].
Ubiquitin (Ub) and Ub-like proteins are typified by a β-grasp fold. Ub-like proteins (Ubl) such as Nedd8 []and SUMO []are also covalently linked to target polypeptides, just as Ub itself. This fold is also found in Ub-related domains, such as the UBX domain []and Ras-binding domain (RBD) [].
Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumour suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8 [, , ].
E1 and E2 enzymes play a central role in ubiquitin and ubiquitin-like protein transfer cascades. This is an E2 binding domain that is found on NEDD8 activating E1 enzyme. The protein resembles ubiquitin, and recruits the catalytic core of the E2 enzyme Ubc12 in a similar manner to that in which ubiquitin interacts with ubiquitin binding domains [].
This entry includes COP9 signalosome complex subunit 9, a component of the COP9 signalosome complex (CSN), which is conserved in all eukaryotes. The CSN complex is an essential regulator of the largest family of E3 ubiquitin ligases, the cullin-RING-ubiquitin ligases (CRLs). The CSN complex deactivates CRL by removing the ubiquitin-like tag NEDD8 (deneddylation) from the cullin subunit, or by binding to the deneddylated CRL, and preventing it interacting with E2 enzymes and ubiquitination substrates [].
This entry represents NEDD8-activating enzyme E1 catalytic subunit from fungi, plants and invertebrates. In budding yeasts, it is also known as Uba3, which is a catalytic subunit of the dimeric Uba3-Ula1 E1 enzyme that activates NEDD8/Rub1 before neddylation, the process by which the ubiquitin-like protein NEDD8 is conjugated to its target proteins []. In C.elegans, Uba3 (also known as rfl-1) is required for cytokinesis and mitotic spindle orientation [].
COP9 signalosome complex subunit 1 (CSN1) is an essential component of the COP9 signalosome complex (CSN), an eight-subunit protein complex that is found in all eukaryotes []. The CSN complex cleaves the isopeptide bond of ubiquitin-like protein Nedd8 from cullins and is involved in various cellular and developmental processes, such as repression of photomorphogenesis in plants and protein subcellular localization, DNA-damage response, and NF-kappaB activation in mammals [, ]. CSN1 carries a C-terminal PCI (for Proteasome, COP9 signalosome, and Initiation factor 3) domain which mediates protein-protein interactions within the complex []. Its N-terminal domain is critical for the function of CSN [].
Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). Enzymatically, CSN functions as an isopeptidase that removes the ubiquitin-like activator NEDD8 from CRLs, but it can also bind deneddylated CRLs and maintain them in an inactive state. The CSN subunits CSN1, CSN2, CSN3, CSN4, CSN7 and CSN8, share a common domain composition: an N-terminal array of tandem α-helical tetratricopeptide/-like repeats, a 34 residue motif, followed by a PCI domain, which encompasses a WH subdomain, a linker, and one or two α-helices at the C terminus. This entry represents the C-terminal helices found on CSN4. The two helices from CSN4 (helices I and II) form a brace roughly perpendicular to the bundle axis in contact with the three C-terminal helices of CSN6. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Both CSN1 and CSN4 are dependent on the presence of their C-terminal helix (CSN1 isoform-2 residues: 466-527; and CSN4: 364-406) for integration into CSN. COP9 signalosome shares common architecture with the 26S proteasome lid and eIF3 where the 19S lid subunit RPN5 and the eIF3 core subunit eIF3a share significant structural similarity with CSN4 [].
Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome [].Ubiquitin is a globular protein, the last four C-terminal residues (Leu-Arg-Gly-Gly) extending from the compact structure to form a 'tail', important for its function. The latter is mediated by the covalent conjugation of ubiquitin to target proteins, by an isopeptide linkage between the C-terminal glycine and the epsilon amino group of lysine residues in the target proteins.Ubiquitin is expressed as three different precursors: a polymeric head-to-tail concatemer of identical units (polyubiquitin), and two N-terminal ubiquitin moieties, UbL40 and UbS27, that are fused to the ribosomal polypeptides L40 and S27, respectively. Specific endopeptidases cleave these precursor molecules []to release ubiquitin moieties that are identical in sequence and contribute to the ubiquitin pool []. Some organisms express additional ubiquitin fusion proteins []. Furthermore, there are several ubiquitin-like proteins derived from ubiquitin [].This entry represents a domain characteristic of ubiquitin (Ub) and ubiquitin-like (Ubl) proteins such as SUMO [, ]and Nedd8 [].
The COP9 signalosome (CSN) is a conserved protein complex that regulates the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes [], which leads to a decrease in Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2 []. Protein kinases CK2 and D, which phosphorylate proteins such as cJun and p53 resulting in their degradation by the ubiquitin-26S proteasome system, also binds to CSN [, ]. The mammalian CSN typically consistis of eight subunits designated CSN1-CSN8. The fission yeast possesses a smaller version of the CSN, consisting only of six subunits, whereas a more distant CSN-like complex has been described in Saccharomyces cerevisiae [].COP9 signalosome complex subunit 5 (Rri1, CSN5 or JAB1) is a metallo-isopeptidase (MEROPS identifier M67.002) that releases the ubiquitin-like protein Nedd8 from the Cul1 subunit of SCF ubiquitin ligases []. Rri1 binds a zinc ion via the histidines in an HXH motif and an aspartic acid C-terminal to this motif []. This entry includes CSN5 homologues from yeast to human.
The COP9 signalosome (CSN) is a conserved protein complex that regulates the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of SCF-type E3 ligase complexes [], which leads to a decrease in Ubl ligase activity of SCF-type complexes such as SCF, CSA or DDB2 []. Protein kinases CK2 and D, which phosphorylate proteins such as cJun and p53 resulting in their degradation by the ubiquitin-26S proteasome system, also binds to CSN [, ]. The mammalian CSN typically consistis of eight subunits designated CSN1-CSN8. The fission yeast possesses a smaller version of the CSN, consisting only of six subunits, whereas a more distant CSN-like complex has been described in Saccharomyces cerevisiae [].CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD; MEROPS identifier M67.972) is one of the eight subunits of COP9 signalosome. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5 []. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6 []. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells []. The cleavage of Rbx1 and increased deneddylation of cullins inactivate CRLs and presumably stabilize pro-apoptotic factors for final apoptotic steps. While CSN6 shows a typical MPN metalloprotease fold, it lacks the canonical JAMM motif, and therefore does not show catalytic isopeptidase activity.
