UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains alpha-helical structural homology ubiquitin-binding domains, including UBA domains and coupling of ubiquitin conjugation to endoplasmic reticulum degradation (CUE) domains which share a common three-helical bundle architecture. UBA domains are commonly occurring sequence motifs found in proteins involved in ubiquitin-mediated proteolysis. They contribute to ubiquitin (Ub) binding or ubiquitin-like (UbL) domain binding. However, some kinds of UBA domains can only bind the UbL domain, but not the Ub domain. UBA domains are normally comprised of compact three-helix bundles which contain a conserved GF/Y-loop. They can bind polyubiquitin with high affinity. They also bind monoubiquitin and other proteins. Most UBA domain-containing proteins have one UBA domain, but some harbor two or three UBA domains. CUE domain containing proteins are characterized by an FP and a di-leucine-like sequence and bind to monoubiquitin with varying affinities. Some higher eukaryotic CUE domain proteins do not bind monoubiquitin efficiently, since they carry LP, rather than FP among CUE domains. This superfamily also includes many UBA-like domains found in AMP-activated protein kinase (AMPK) related kinases, the NXF family of mRNA nuclear export factors, elongation factor Ts (EF-Ts), nascent polypeptide-associated complex subunit alpha (NACA) and similar proteins. Although many UBA-like domains may have a conserved TG but not GF/Y-loop, they still show a high level of structural and sequence similarity with three-helical ubiquitin binding domains.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 73919015   2 NKLKSStHRDKVKKFISLTHTGEQTAIFCLQQNDWKFELASDNYFQNP 49
Cdd:cd14412   1 HKLKSS-QKDKVRQFMAFTQAGERTAIYCLTQNEWKLEVATDNYFQNP 47

UBA-like domain found in DCN1-like protein 2 (DCNL2) and similar proteins; DCNL2 (defective in cullin neddylation protein 1-like protein 2), also called DCUN1 domain-containing protein 2, is encoded by gene DCUN1D2. Although its biological function remains unclear, DCNL2 shows high sequence similarity with DCNL1, a protein that plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. At this point, DCNL2 may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that is responsible for the binding to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 73919015   2 NKLKSStHRDKVKKFISLTHTGEQTAIFCLQQNDWKFELASDNYFQNP 49
Cdd:cd14412   1 HKLKSS-QKDKVRQFMAFTQAGERTAIYCLTQNEWKLEVATDNYFQNP 47

UBA-like domain found in DCN1-like protein 2 (DCNL2) and similar proteins; DCNL2 (defective in cullin neddylation protein 1-like protein 2), also called DCUN1 domain-containing protein 2, is encoded by gene DCUN1D2. Although its biological function remains unclear, DCNL2 shows high sequence similarity with DCNL1, a protein that plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. At this point, DCNL2 may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that is responsible for the binding to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*...
gi 73919015   2 NKLKSStHRDKVKKFISLTHTGEQTAIFCLQQNDWKFELASDNYFQNP 49
Cdd:cd14412   1 HKLKSS-QKDKVRQFMAFTQAGERTAIYCLTQNEWKLEVATDNYFQNP 47

UBA-like domain found in DCN1-like protein 1 (DCNL1) and similar proteins; DCNL1 (defective in cullin neddylation protein 1-like protein 1), also called DCUN1 domain-containing protein 1, is encoded by squamous cell carcinoma-related oncogene SCCRO (DCUN1D1). It interacts with known cullin isoforms as well as ROC1, Ubc12 and CAND1, the components of the neddylation pathway. It plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. DCNL1 contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal cullin binding domain that binds to cullins and Rbx-1, components of an E3 ubiquitin ligase complex for neddylation.

                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 73919015   1 MNKLKSStHRDKVKKFISLTHTGEQTAIFCLQQNDWKFELASDNYFQNPEYY 52
Cdd:cd14411   1 MNKLKSS-QKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 51

UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; This family includes nuclear RNA export factors (NXF1/NXF2), FAS-associated factors (FAF1/2), tyrosyl-DNA phosphodiesterase 2 (TDP2), OTU domain-containing proteins (OTU7A/OTU7B), NSFL1 cofactor p47, defective in cullin neddylation protein 1 (DCN1)-like protein (DCNL1/DCNL2), yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins. NXF proteins can stimulate nuclear export of mRNAs and facilitate the export of unspliced viral mRNA containing the constitutive transport element. FAF1 is an apoptotic signaling molecule that acts downstream in the Fas signal transduction pathway. It interacts with the cytoplasmic domain of Fas, but not to a Fas mutant that is deficient in signal transduction. FAF2 is the translation product of a highly expressed gene in the T-cells and eosinophils of atopic dermatitis patients compared with those of normal individuals. Its biological function remains unclear. TDP2 is a 5'-Tyr-DNA phosphodiesterase required for the efficient repair of topoisomerase II-induced DNA double strand breaks. OTU7A and OTU7B are zinc finger proteins that function as deubiquitinating enzymes. p47 is a major cofactor of the cytosolic AAA ATPase p97. It is required for the p97-regulated membrane reassembly of the endoplasmic reticulum (ER), the nuclear envelope and the Golgi apparatus. DCNL1 plays an essential role in the neddylation E3 complex and participates in the release of inhibitory effects of CAND1 on cullin-RING ligase E3 complex assembly and activity. The biological function of DCNL2 remains unclear. Yeast DCN1 is a scaffold-type E3 ligase for cullin neddylation. It can bind directly to cullins and the ubiquitin-like protein Nedd8-specific E2 (Ubc12), and regulate cullin neddylation and thus display ubiquitin ligase activity.

                        10        20        30
                ....*....|....*....|....*....|.
gi 73919015  16 FISLTHTGEQTAIFCLQQNDWKFELASDNYF 46
Cdd:cd14273   1 FMEITGADPETARQYLESNNWDLEAAINLYF 31

UBA-like domain found in Caenorhabditis elegans tyrosyl-DNA phosphodiesterase 2 (TDP2) and similar proteins; The family includes C. elegans TDP2 and its homologs found in bilateria. TDP2 (also known as TTRAP or EAPII) belongs to the Mg(2+)/Mn(2+)-dependent family of phosphodiesterases which contains an N-terminal ubiquitin-associated (UBA)-like domain and a C-terminal phosphodiesterase domain. It required for the efficient repair of topoisomerase II-induced DNA double strand breaks. The topoisomerase is covalently linked by a phosphotyrosyl bond to the 5'-terminus of the break. TDP2 cleaves the DNA 5'-phosphodiester bond and restores 5'-phosphate termini needed for subsequent DNA ligation and hence repair of the break. Tyrosyl-DNA phosphodiesterase 1 (TDP1), an enzyme that cleaves 3'-phosphotyrosyl bonds, and TDP2 are complementary activities; together, they allow cells to remove trapped topoisomerase from both 3'- and 5'-DNA termini. TDP2 has been reported as being involved in apoptosis, embryonic development, and transcriptional regulation.

                        10        20        30
                ....*....|....*....|....*....|....*..
gi 73919015  11 DKVKKFISLTHTGEQTAIFCLQQNDWKFELASDNYFQ 47
Cdd:cd14672   1 QLCEEFAEITGTDEALAQFYLQDRDWDLEKALDVYFG 37