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Conserved domains on  [gi|1958750456|ref|XP_038958168|]
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DCN1-like protein 1 isoform X4 [Rattus norvegicus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UBA_like_SF super family cl21463
UBA domain-like superfamily; The ubiquitin-associated (UBA) domain-like superfamily contains ...
 15-65 1.15e-26

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.


The actual alignment was detected with superfamily member cd14411:

Pssm-ID: 473871  Cd Length: 51  Bit Score: 96.38  E-value: 1.15e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958750456  15 LNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 65
Cdd:cd14411     1 MNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 51
Cullin_binding super family cl04154
Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ...
 150-189 1.87e-10

Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices.


The actual alignment was detected with superfamily member pfam03556:

Pssm-ID: 460971  Cd Length: 117  Bit Score: 56.05  E-value: 1.87e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958750456 150 KLKAQIPKMEQELKEPGR-FKDFYQFTFNFAKNPGQKGLGM 189
Cdd:pfam03556   1 KLKAKLPELRKELTDPSEyFKKVYRFTFDFAKEPGQKSLDL 41
 
Name Accession Description Interval E-value
UBA_DCNL1 cd14411
UBA-like domain found in DCN1-like protein 1 (DCNL1) and similar proteins; DCNL1 (defective in ...
 15-65 1.15e-26

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.


Pssm-ID: 270594  Cd Length: 51  Bit Score: 96.38  E-value: 1.15e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958750456  15 LNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 65
Cdd:cd14411     1 MNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 51
Cullin_binding pfam03556
Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ...
 150-189 1.87e-10

Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices.


Pssm-ID: 460971  Cd Length: 117  Bit Score: 56.05  E-value: 1.87e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958750456 150 KLKAQIPKMEQELKEPGR-FKDFYQFTFNFAKNPGQKGLGM 189
Cdd:pfam03556   1 KLKAKLPELRKELTDPSEyFKKVYRFTFDFAKEPGQKSLDL 41
UBA_4 pfam14555
UBA-like domain;
23-63 1.66e-08

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 48.60  E-value: 1.66e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958750456  23 KDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPE 63
Cdd:pfam14555   1 DELIAQFQAITGADEEVARQYLEAHNWDLEAAVNAFFDDGE 41
 
Name Accession Description Interval E-value
UBA_DCNL1 cd14411
UBA-like domain found in DCN1-like protein 1 (DCNL1) and similar proteins; DCNL1 (defective in ...
 15-65 1.15e-26

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.


Pssm-ID: 270594  Cd Length: 51  Bit Score: 96.38  E-value: 1.15e-26
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1958750456  15 LNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 65
Cdd:cd14411     1 MNKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPELY 51
UBA_DCNL2 cd14412
UBA-like domain found in DCN1-like protein 2 (DCNL2) and similar proteins; DCNL2 (defective in ...
 16-62 7.94e-24

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.


Pssm-ID: 270595  Cd Length: 47  Bit Score: 88.98  E-value: 7.94e-24
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1958750456  16 NKLKSSQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNP 62
Cdd:cd14412     1 HKLKSSQKDKVRQFMAFTQAGERTAIYCLTQNEWKLEVATDNYFQNP 47
UBA_DCNL cd14350
UBA-like domain found in DCN1-like protein DCNL1, DCNL2 and similar proteins; DCNL1 (defective ...
 21-62 1.37e-19

UBA-like domain found in DCN1-like protein DCNL1, DCNL2 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. 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 and may also contribute to neddylation of cullin components of SCF-type E3 ubiquitin ligase complexes. Like DCNL1, DCNL2 contains an N-terminal UBA-like domain and a C-terminal cullin binding domain.


Pssm-ID: 270535  Cd Length: 42  Bit Score: 77.68  E-value: 1.37e-19
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1958750456  21 SQKDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNP 62
Cdd:cd14350     1 SQKDKVRQFMSITQANEKTAIQCLKDADWNLELAVDAYFQNP 42
Cullin_binding pfam03556
Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ...
 150-189 1.87e-10

Cullin binding; This domain binds to cullins and to Rbx-1, components of an E3 ubiquitin ligase complex for neddylation. Neddylation is the process by which the C-terminal glycine of the ubiquitin-like protein Nedd8 is covalently linked to lysine residues in a protein through an isopeptide bond. The structure of this domain is composed entirely of alpha helices.


Pssm-ID: 460971  Cd Length: 117  Bit Score: 56.05  E-value: 1.87e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958750456 150 KLKAQIPKMEQELKEPGR-FKDFYQFTFNFAKNPGQKGLGM 189
Cdd:pfam03556   1 KLKAKLPELRKELTDPSEyFKKVYRFTFDFAKEPGQKSLDL 41
UBA_4 pfam14555
UBA-like domain;
23-63 1.66e-08

UBA-like domain;


Pssm-ID: 464207  Cd Length: 43  Bit Score: 48.60  E-value: 1.66e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1958750456  23 KDKVRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFFQNPE 63
Cdd:pfam14555   1 DELIAQFQAITGADEEVARQYLEAHNWDLEAAVNAFFDDGE 41
UBA_TAP-C_like cd14273
UBA-like domain found in the NXF family of mRNA nuclear export factors and similar proteins; ...
 29-59 1.35e-06

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.


Pssm-ID: 270459  Cd Length: 31  Bit Score: 43.16  E-value: 1.35e-06
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958750456  29 FMIFTQSSEKTAVSCLSQNDWKLDVATDNFF 59
Cdd:cd14273     1 FMEITGADPETARQYLESNNWDLEAAINLYF 31
UBA_DCN1 cd14352
UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar ...
 26-59 2.42e-06

UBA-like domain found in yeast defective in cullin neddylation protein 1 (DCN1) and similar proteins; 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. It contains an N-terminal ubiquitin-associated (UBA)-like domain and a unique C-terminal PONY domain that is essential for the neddylation function of DCN1.


Pssm-ID: 270537  Cd Length: 36  Bit Score: 42.66  E-value: 2.42e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958750456  26 VRQFMIFTQSSEKTAVSCLSQNDWKLDVATDNFF 59
Cdd:cd14352     3 IKQFREITATSPEVARDYLQRSNWNLNYAVDDFY 36
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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