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Conserved domains on  [gi|1958661782|ref|XP_038943060|]
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ubiquitin domain-containing protein 2 isoform X1 [Rattus norvegicus]

Protein Classification

ubiquitin domain-containing protein( domain architecture ID 13872716)

ubiquitin domain-containing protein; similar to Danio rerio ubiquitin domain-containing protein 1 (UBTD1) that may be involved in the regulation of cellular senescence; contains a ubiquitin-binding (UBD) domain

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
UBD pfam16455
Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin ...
 1-88 8.12e-52

Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin domain-containing proteins.


:

Pssm-ID: 465122  Cd Length: 101  Bit Score: 161.60  E-value: 8.12e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958661782   1 MTDGQLRSKRDEFWDTApaFEGRKEIWDALKAAAHAFESNDHELAQAIIDGANITLPHGALTE-CYDELGNRYQLPVYCL 79
Cdd:pfam16455  15 WTRAQLDRERDEFFDTR--VTGRPEIWDALRAAAEVLEEGDLATAQAILDAAGITLPTGDLTDgCYDELGNLYRLPEYVV 92


                  ....*....
gi 1958661782  80 APPINMIEE 88
Cdd:pfam16455  93 SDPTNLIED 101
Ubl_UBTD2 cd17121
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, ...
 107-181 3.57e-51

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, also termed dendritic cell-derived ubiquitin-like protein (DC-UbP), or ubiquitin-like protein SB72, is a potential ubiquitin shuttle protein firstly identified in dendritic cells and implicated in apoptosis. It binds proteins involved in the ubiquitination pathway and may play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells. UBTD2 is expressed in tumor cells but not in normal human adult tissue suggesting a role in tumorogenesis. It can potentially regulate the stability of proteins involved in various physiological processes relevant to many disease phenotypes, such as ageing and cancer. UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes.


:

Pssm-ID: 340641  Cd Length: 75  Bit Score: 158.98  E-value: 3.57e-51
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958661782 107 ESQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 181
Cdd:cd17121     1 ECQLRLRLSTGKDLKLAVRSTDTVYHMKRRLHTAEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 75
 
Name Accession Description Interval E-value
UBD pfam16455
Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin ...
 1-88 8.12e-52

Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin domain-containing proteins.


Pssm-ID: 465122  Cd Length: 101  Bit Score: 161.60  E-value: 8.12e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958661782   1 MTDGQLRSKRDEFWDTApaFEGRKEIWDALKAAAHAFESNDHELAQAIIDGANITLPHGALTE-CYDELGNRYQLPVYCL 79
Cdd:pfam16455  15 WTRAQLDRERDEFFDTR--VTGRPEIWDALRAAAEVLEEGDLATAQAILDAAGITLPTGDLTDgCYDELGNLYRLPEYVV 92


                  ....*....
gi 1958661782  80 APPINMIEE 88
Cdd:pfam16455  93 SDPTNLIED 101
Ubl_UBTD2 cd17121
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, ...
 107-181 3.57e-51

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, also termed dendritic cell-derived ubiquitin-like protein (DC-UbP), or ubiquitin-like protein SB72, is a potential ubiquitin shuttle protein firstly identified in dendritic cells and implicated in apoptosis. It binds proteins involved in the ubiquitination pathway and may play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells. UBTD2 is expressed in tumor cells but not in normal human adult tissue suggesting a role in tumorogenesis. It can potentially regulate the stability of proteins involved in various physiological processes relevant to many disease phenotypes, such as ageing and cancer. UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes.


Pssm-ID: 340641  Cd Length: 75  Bit Score: 158.98  E-value: 3.57e-51
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958661782 107 ESQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 181
Cdd:cd17121     1 ECQLRLRLSTGKDLKLAVRSTDTVYHMKRRLHTAEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 75
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 110-181 3.28e-13

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 61.80  E-value: 3.28e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958661782 110 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 181
Cdd:pfam00240   1 ITVKTLDGKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 109-179 1.23e-08

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 49.56  E-value: 1.23e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958661782  109 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVS 179
Cdd:smart00213   2 ELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
PTZ00044 PTZ00044
ubiquitin; Provisional
 109-177 2.94e-05

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 40.58  E-value: 2.94e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958661782 109 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKI-PKDYVVQVI 177
Cdd:PTZ00044    2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVvPGSTIHMVL 71
 
Name Accession Description Interval E-value
UBD pfam16455
Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin ...
 1-88 8.12e-52

Ubiquitin-binding domain; This ubiquitin-binding domain is found in ubiquitin domain-containing proteins.


Pssm-ID: 465122  Cd Length: 101  Bit Score: 161.60  E-value: 8.12e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958661782   1 MTDGQLRSKRDEFWDTApaFEGRKEIWDALKAAAHAFESNDHELAQAIIDGANITLPHGALTE-CYDELGNRYQLPVYCL 79
Cdd:pfam16455  15 WTRAQLDRERDEFFDTR--VTGRPEIWDALRAAAEVLEEGDLATAQAILDAAGITLPTGDLTDgCYDELGNLYRLPEYVV 92


                  ....*....
gi 1958661782  80 APPINMIEE 88
Cdd:pfam16455  93 SDPTNLIED 101
Ubl_UBTD2 cd17121
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, ...
 107-181 3.57e-51

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 2 (UBTD2); UBTD2, also termed dendritic cell-derived ubiquitin-like protein (DC-UbP), or ubiquitin-like protein SB72, is a potential ubiquitin shuttle protein firstly identified in dendritic cells and implicated in apoptosis. It binds proteins involved in the ubiquitination pathway and may play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells. UBTD2 is expressed in tumor cells but not in normal human adult tissue suggesting a role in tumorogenesis. It can potentially regulate the stability of proteins involved in various physiological processes relevant to many disease phenotypes, such as ageing and cancer. UBTD2 reconciles protein ubiquitination and deubiquitination via linking UbE1 and USP5 enzymes.


Pssm-ID: 340641  Cd Length: 75  Bit Score: 158.98  E-value: 3.57e-51
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958661782 107 ESQLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 181
Cdd:cd17121     1 ECQLRLRLSTGKDLKLAVRSTDTVYHMKRRLHTAEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 75
Ubl_UBTD cd01794
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and ...
 110-178 6.90e-43

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing proteins UBTD1, UBTD2, and similar proteins; This family represents a group of ubiquitin-like (Ubl) domain-containing proteins evolutionarily conserved and found in metazoa, fungi, and plants. They may regulate the activity and/or specificity of E2 ubiquitin conjugating enzymes belonging to the UBE2D family. Members in this family contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions.


Pssm-ID: 340492  Cd Length: 69  Bit Score: 137.80  E-value: 6.90e-43
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958661782 110 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIV 178
Cdd:cd01794     1 LKLRLSTGKDLKLSVRSTDTVLQAKRRLQALEGIEPSRQRWFFSGKLLTDKTRIEDAKIPKGFVVQVIV 69
Ubl_UBTD1 cd17120
ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is ...
 110-178 1.27e-31

ubiquitin-like (Ubl) domain found in ubiquitin domain-containing protein 1 (UBTD1); UBTD1 is the mammalian homolog of the mitochondrial Dc-UbP/UBTD2 protein, both of which contain an N-terminal ubiquitin binding domain (UBD) and a C-terminal ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. UBTD1 stably interacts with the UBE2D family of E2 ubiquitin conjugating enzymes. As a tumor suppressor, UBTD1 plays a pivotal role in in regulating cellular senescence that mediates p53 function. It is also involved in MDM2 ubiquitination and degradation.


Pssm-ID: 340640  Cd Length: 69  Bit Score: 109.25  E-value: 1.27e-31
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958661782 110 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIV 178
Cdd:cd17120     1 LKVRLSTGKDVRLSASMSDTIGQLKKQLHAQEGIEPSWQRWFFSGKLLTDKTRLQETKIQKDFVIQVIV 69
Ubl_ubiquitin_like cd17039
ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like ...
 110-177 1.06e-14

ubiquitin-like (Ubl) domain found in ubiquitin and ubiquitin-like Ubl proteins; Ubiquitin-like (Ubl) proteins have a similar ubiquitin (Ub) beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ub and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Some Ubl domains have adaptor roles in Ub-signaling by mediating protein-protein interaction. Prokaryotic sulfur carrier proteins are Ub-related proteins that can be activated in an ATP-dependent manner. Polyubiquitination signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. One of these seven lysine residues (K27, Ub numbering) is conserved in this Ubl_ubiquitin_like family. K27-linked Ub chains are versatile and can be recognized by several downstream receptor proteins. K27 has roles beyond chain linkage, such as in Ubl NEDD8 (which contains many of the same lysines (K6, K11, K27, K33, K48) as Ub) where K27 has a role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340559 [Multi-domain]  Cd Length: 68  Bit Score: 65.70  E-value: 1.06e-14
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1958661782 110 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVI 177
Cdd:cd17039     1 ITVKTLDGKTYTVEVDPDDTVADLKEKIEEKTGIPVEQQRLIYNGKELKDDKTLSDYGIKDGSTIHLV 68
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 110-181 3.28e-13

Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog), Nedd8, Elongin B, Rub1, and Parkin. A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites.


Pssm-ID: 459726 [Multi-domain]  Cd Length: 72  Bit Score: 61.80  E-value: 3.28e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1958661782 110 LRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVSQP 181
Cdd:pfam00240   1 ITVKTLDGKKITLEVDPTDTVLELKEKIAEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVLRQR 72
Ubl_NEDD8 cd01806
ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally ...
 116-168 1.09e-08

ubiquitin-like (Ubl) domain found in neural precursor cell expressed developmentally down-regulated protein 8 (NEDD8) and similar proteins; NEDD8, also termed Neddylin, or RELATED TO UBIQUITIN (RUB/Rub1p) in plant and yeast, is a ubiquitin-like protein that conjugates to nuclear proteins in a manner analogous to ubiquitination and sentrinization. It 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. NEDD8 deamidation and its inhibition of Cullin-RING ubiquitin ligases (CRLs) activity are responsible for Cycle-inhibiting factor (Cif)/Cif homolog in Burkholderia pseudomallei (CHBP)-induced cytopathic effect. NEDD8 contains a single conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. Polyubiquitination, signals for a diverse set of cellular events via different isopeptide linkages formed between the C terminus of one ubiquitin (Ub) and the epsilon-amine of K6, K11, K27, K29, K33, K48, or K63 of a second Ub. Ubl NEDD8, contains many of the same lysines (K6, K11, K27, K33, K48) as Ub, where K27 has an role (other than conjugation) in the mechanism of protein neddylation.


Pssm-ID: 340504 [Multi-domain]  Cd Length: 74  Bit Score: 50.08  E-value: 1.09e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1958661782 116 TGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKI 168
Cdd:cd01806     7 TGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIFSGKQMNDEKTAADYKI 59
UBQ smart00213
Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of ...
 109-179 1.23e-08

Ubiquitin homologues; Ubiquitin-mediated proteolysis is involved in the regulated turnover of proteins required for controlling cell cycle progression


Pssm-ID: 214563 [Multi-domain]  Cd Length: 72  Bit Score: 49.56  E-value: 1.23e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1958661782  109 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIVS 179
Cdd:smart00213   2 ELTVKTLDGKTITLEVKPSDTVSELKEKIAELTGIPPEQQRLIYKGKVLEDDRTLADYGIQDGSTIHLVLR 72
Ubl2_ISG15 cd01810
ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar ...
 124-168 3.58e-07

ubiquitin-like (Ubl) domain 2 found in interferon-stimulated gene 15 (ISG15) and similar proteins; ISG15, also termed interferon-induced 15 kDa protein, or interferon-induced 17 kDa protein (IP17), or ubiquitin cross-reactive protein (UCRP), is an antiviral interferon-induced ubiquitin-like protein that upon viral infection it modifies cellular and viral proteins by mechanisms similar to ubiquitination. Although ISG15 has properties similar to those of other ubiquitin-like (Ubl) molecules, it is a unique member of the Ubl superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system. ISG15 contains two tandem Ubl domains with a beta-grasp Ubl fold. This family corresponds to the second Ubl domain.


Pssm-ID: 340508 [Multi-domain]  Cd Length: 74  Bit Score: 45.91  E-value: 3.58e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1958661782 124 VRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKI 168
Cdd:cd01810    17 VRLTQTVDQLKQKVSGREGVHDDQFWLTFEGRPLEDQLPLGEYGL 61
Ubl_ubiquitin cd01803
ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes ...
 109-171 1.94e-06

ubiquitin-like (Ubl) domain found in ubiquitin; Ubiquitin is a protein modifier in eukaryotes that is involved in various cellular processes, including transcriptional regulation, cell cycle control, and DNA repair. Ubiquitination is comprised of a cascade of E1, E2 and E3 enzymes that results in a covalent bond between the C-terminus of ubiquitin and the epsilon-amino group of a substrate lysine. Ubiquitin-like (Ubl) proteins have similar ubiquitin beta-grasp fold and attach to other proteins in a Ubl manner but with biochemically distinct roles. Ubiquitin (Ub)and Ubl proteins conjugate and deconjugate via ligases and peptidases to covalently modify target polypeptides. Ub includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains.


Pssm-ID: 340501 [Multi-domain]  Cd Length: 76  Bit Score: 43.97  E-value: 1.94e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1958661782 109 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKD 171
Cdd:cd01803     2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKE 64
Ubl_UBLCP1 cd01813
ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 ...
 117-168 5.97e-06

ubiquitin-like (Ubl) domain found in ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) and similar proteins; UBLCP1 is a 26S proteasome phosphatase that regulates nuclear proteasome activity. It is localized in the nucleus and it contains conserved ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold, which directly interacts with the proteasome. Knockdown of UBLCP1 in cells promotes 26S proteasome assembly and selectively enhances nuclear proteasome activity. UBLCP1 may also play a role in the regulation of phosphorylation state of RNA polymerase II C-terminal domain, a key event during mRNA metabolism.


Pssm-ID: 340511  Cd Length: 74  Bit Score: 42.56  E-value: 5.97e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1958661782 117 GKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWF---FSGRPLTDKMKLEELKI 168
Cdd:cd01813     9 GKEYPVTVLSSDTVLDLKQRIFELTGVLPKRQKLLglkVKGKPADDDVKLSSLKL 63
Ubl_USP48 cd01795
ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and ...
 113-190 2.20e-05

ubiquitin-like (Ubl) domain found in ubiquitin-specific-processing protease 48 (USP48) and similar proteins; USP48, also termed USP31, or deubiquitinating enzyme 48, or ubiquitin thioesterase 48, or ubiquitin carboxyl-terminal hydrolase 48, belongs to the ubiquitin specific protease (USP) family that is one of at least seven deubiquitylating enzyme (DUB) families capable of deconjugating ubiquitin (Ub)and ubiquitin-like (Ubl) adducts. While the USP proteins have a conserved catalytic core domain, USP48 differs in its domain architecture. It contains an N-terminal USP domain, three DUSP (domain present in ubiquitin-specific protease) domains, and a C-terminal Ubl domain with a beta-grasp Ubl fold, a common structure involved in protein-protein interactions. USP48 is a deubiquitinating enzyme that interacts with TNF receptor-associated factor 2 (TRAF2) and has been implicated in activation of nuclear factor-kappaB (NF-kappaB). Moreover, as a nuclear deubiquitinase regulated by casein kinase 2 (CK2), USP48 controls the ubiquitin/proteasome-system (UPS)-dependent turnover of activated NF-kappaB/RelA in the nucleus together with the COP9 signalosome, suggesting a role of USP48 in a timely control of immune responses.


Pssm-ID: 340493 [Multi-domain]  Cd Length: 99  Bit Score: 41.50  E-value: 2.20e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1958661782 113 RLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTD-KMKLEELKIPKDYVVQVIVSQPVQNPAPVEN 190
Cdd:cd01795     1 RRVRGERKSLTVSSTTTLKELKLQIMEKFSVAPFDQHLYFNGRELTDdSATLADLGILPGDVLYLKVDEPPDDPDDADE 79
PTZ00044 PTZ00044
ubiquitin; Provisional
 109-177 2.94e-05

ubiquitin; Provisional


Pssm-ID: 185411 [Multi-domain]  Cd Length: 76  Bit Score: 40.58  E-value: 2.94e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958661782 109 QLRLRLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKI-PKDYVVQVI 177
Cdd:PTZ00044    2 QILIKTLTGKKQSFNFEPDNTVQQVKMALQEKEGIDVKQIRLIYSGKQMSDDLKLSDYKVvPGSTIHMVL 71
Ubl_FUBI cd01793
ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is ...
 122-178 1.98e-03

ubiquitin-like (Ubl) domain found in ubiquitin-like protein FUBI and similar proteins; FUBI is a pro-apoptotic regulatory gene FAU encoding ubiquitin-like protein with ribosomal protein S30 as a C-terminal extension. FUBI functions as a tumor suppressor protein that may be involved in the ATP-dependent proteolytic activity of ubiquitin. The N-terminal ubiquitin-like (Ubl) domain of FUBI has the beta-grasp Ubl fold, and it may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.


Pssm-ID: 340491  Cd Length: 74  Bit Score: 35.72  E-value: 1.98e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958661782 122 LVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIV 178
Cdd:cd01793    13 LEVSGNETVADIKAHIAALEGIAVEDQVLLYAGAPLEDDVVLGQCGIPDLATLEVAV 69
Ubl_UHRF1 cd17122
ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing ...
 130-178 6.58e-03

ubiquitin-like (Ubl) domain found in ubiquitin-like PHD and RING finger domain-containing protein 1(UHRF1); UHRF1, also termed inverted CCAAT box-binding protein of 90 kDa, or nuclear protein 95, or nuclear zinc finger protein Np95 (Np95), or RING finger protein 106, or transcription factor ICBP90, or E3 ubiquitin-protein ligase UHRF1, is a unique chromatin effector protein that integrates the recognition of both histone PTMs and DNA methylation. It is essential for cell proliferation and plays a critical role in the development and progression of many human carcinomas, such as laryngeal squamous cell carcinoma, gastric cancer, esophageal squamous cell carcinoma, colorectal cancer, prostate cancer, and breast cancer. UHRF1 can acts as a transcriptional repressor through its binding to histone H3 when it is unmodified at Arg2. Its overexpression in human lung fibroblasts results in downregulation of expression of the tumor suppressor pRB. It also plays a role in transcriptional repression of the cell cycle regulator p21.Moreover, UHRF1-dependent repression of factors can facilitate the G1-S transition. It interacts with Tat-interacting protein of 60 kDa (TIP60) and induces degradation-independent ubiquitination ofTIP60. It is also an N-methylpurine DNA glycosylase (MPG)-interacting protein that binds MPG in a p53status-independent manner in the DNA base excision repair (BER) pathway. In addition, UHRF1 functions as an epigenetic regulator that is important for multiple aspects of epigenetic regulation, including maintenance of DNA methylation patterns and recognition of various histone modifications. UHRF1 contains an N-terminal ubiquitin-like domain (Ubl), a tandem Tudor domain (TTD), a plant homeodomain (PHD) finger, a SET and RING finger associated (SRA) domain, and a C-terminal RING-finger domain. It specifically binds to hemimethylated DNA, double-stranded CpG dinucleotides, and recruits the maintenance methyltransferase DNMT1 to its hemimethylated DNA substrate through its SRA domain. UHRF1-dependent H3K23 ubiquitination has an essential role in maintenance DNA methylation and replication. The tandem Tudor domain directs UHRF1 binding to the heterochromatin mark histone H3K9me3 and the PHD finger targets UHRF1 to unmodified histone H3 in euchromatic regions. The RING-finger domain exhibits both autocatalytic E3 ubiquitin (Ub) ligase activity and activity against histone H3 and DNMT1.


Pssm-ID: 340642  Cd Length: 74  Bit Score: 34.08  E-value: 6.58e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1958661782 130 VFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKIPKDYVVQVIV 178
Cdd:cd17122    25 VEELRQKIQELFGVEPERQRLFYRGKQMEDGHTLFDYSVGLNDIVQLLV 73
Ubl_Dsk2p_like cd16106
ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein ...
 113-168 9.76e-03

ubiquitin-like (Ubl) domain found in Saccharomyces cerevisiae proteasome interacting protein Dsk2p and similar proteins; The family contains several fungal multiubiquitin receptors, including Saccharomyces cerevisiae Dsk2p and Schizosaccharomyces pombe Dph1p, both of which have been characterized as shuttle proteins transporting ubiquitinated substrates destined for degradation from the E3 ligase to the 26S proteasome. They interact with the proteasome through their N-terminal ubiquitin-like domain (Ubl) and with ubiquitin (Ub) through their C-terminal Ub-associated domain (UBA). S. cerevisiae Dsk2p is a nuclear-enriched protein that may involve in the ubiquitin-proteasome proteolytic pathway through interacting with K48-linked polyubiquitin and the proteasome. Moreover, it has been implicated in spindle pole duplication through assisting in Cdc31 assembly into the new spindle pole body (SPB). S. pombe Dph1p is an ubiquitin (Ub0 receptor working in concert with the class V myosin, Myo52, to target the degradation of the S. pombe CLIP-170 homolog, Tip1. It also can protect Ub chains against disassembly by deubiquitinating enzymes.


Pssm-ID: 340523 [Multi-domain]  Cd Length: 73  Bit Score: 33.77  E-value: 9.76e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1958661782 113 RLSTGKDLKLVVRSTDTVFHMKRRLHATEGVEPGSQRWFFSGRPLTDKMKLEELKI 168
Cdd:cd16106     6 KCSNGKKFTVEVEPDATVLELKELIAEKSDIPAEQQRLIYKGKILKDEETLSSYKI 61
 
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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