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Conserved domains on  [gi|1317840664|ref|NP_001346129|]
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ubiquitin-like protein 3 isoform b [Mus musculus]

Protein Classification

ubiquitin family protein( domain architecture ID 1000087)

ubiquitin family protein belongs to an diverse class of protein modifier and gene expression regulatory proteins that participate in a number of cellular processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ubl1_cv_Nsp3_N-like super family cl28922
first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV ...
 1-47 3.28e-33

first ubiquitin-like (Ubl) domain located at the N-terminus of coronavirus SARS-CoV non-structural protein 3 (Nsp3) and related proteins; This ubiquitin-like (Ubl) domain (Ubl1) is found at the N-terminus of coronavirus Nsp3, a large multi-functional multi-domain protein which is an essential component of the replication/transcription complex (RTC). The functions of Ubl1 in CoVs are related to single-stranded RNA (ssRNA) binding and to interacting with the nucleocapsid (N) protein. SARS-CoV Ubl1 has been shown to bind ssRNA having AUA patterns, and since the 5'-UTR of the SARS-CoV genome has a number of AUA repeats, it may bind there. In mouse hepatitis virus (MHV), this Ubl1 domain binds the cognate N protein. Adjacent to Ubl1 is a Glu-rich acidic region (also referred to as hypervariable region, HVR); Ubl1 together with HVR has been called Nsp3a. Currently, the function of HVR in CoVs is unknown. This model corresponds to one of two Ubl domains in Nsp3; the other is located N-terminal to the papain-like protease (PLpro) and is not represented by this model.


The actual alignment was detected with superfamily member cd17048:

Pssm-ID: 475130  Cd Length: 82  Bit Score: 109.01  E-value: 3.28e-33
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1317840664  1 MDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 47
Cdd:cd17048   36 EDWEEEQVSSANILRLIYQGRFLHGNVTLGALQLPLGKTTVMHLVAR 82
 
Name Accession Description Interval E-value
Ubl_UBL3 cd17048
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; ...
 1-47 3.28e-33

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; UBL3, also termed membrane-anchored ubiquitin-fold protein (MUB), or protein HCG-1, belongs to a newly described MUB protein family with structural homology with ubiquitin. MUB proteins have a beta-grasp ubiquitin-like (Ubl) domain with longer N- and C-termini and extended loops. The Ubl domain contains a C-terminal CAAX-box, a canonical motif for protein prenylation, which is modified through protein lipidation with a hydrophobic membrane anchor. The lipidation and membrane localization inhibit attachment of MUBs to target proteins.


Pssm-ID: 340568  Cd Length: 82  Bit Score: 109.01  E-value: 3.28e-33
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1317840664  1 MDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 47
Cdd:cd17048   36 EDWEEEQVSSANILRLIYQGRFLHGNVTLGALQLPLGKTTVMHLVAR 82
Rad60-SLD_2 pfam13881
Ubiquitin-2 like Rad60 SUMO-like;
1-70 3.52e-31

Ubiquitin-2 like Rad60 SUMO-like;


Pssm-ID: 372780  Cd Length: 111  Bit Score: 104.70  E-value: 3.52e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1317840664   1 MDWEEeQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKT----TVMHLVARETLPEPNSQGQRNREKTGESNCC 70
Cdd:pfam13881  39 KDKEN-GPKTVNDVKLINAGKILENNKTLGECRLPVGETpggvTTMHVVVRPNLPEPNSEKKANKPKQNGCGCC 111
 
Name Accession Description Interval E-value
Ubl_UBL3 cd17048
ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; ...
 1-47 3.28e-33

ubiquitin-like (Ubl) domain found in ubiquitin-like protein 3 (UBL3) and similar proteins; UBL3, also termed membrane-anchored ubiquitin-fold protein (MUB), or protein HCG-1, belongs to a newly described MUB protein family with structural homology with ubiquitin. MUB proteins have a beta-grasp ubiquitin-like (Ubl) domain with longer N- and C-termini and extended loops. The Ubl domain contains a C-terminal CAAX-box, a canonical motif for protein prenylation, which is modified through protein lipidation with a hydrophobic membrane anchor. The lipidation and membrane localization inhibit attachment of MUBs to target proteins.


Pssm-ID: 340568  Cd Length: 82  Bit Score: 109.01  E-value: 3.28e-33
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1317840664  1 MDWEEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHLVAR 47
Cdd:cd17048   36 EDWEEEQVSSANILRLIYQGRFLHGNVTLGALQLPLGKTTVMHLVAR 82
Rad60-SLD_2 pfam13881
Ubiquitin-2 like Rad60 SUMO-like;
1-70 3.52e-31

Ubiquitin-2 like Rad60 SUMO-like;


Pssm-ID: 372780  Cd Length: 111  Bit Score: 104.70  E-value: 3.52e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1317840664   1 MDWEEeQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKT----TVMHLVARETLPEPNSQGQRNREKTGESNCC 70
Cdd:pfam13881  39 KDKEN-GPKTVNDVKLINAGKILENNKTLGECRLPVGETpggvTTMHVVVRPNLPEPNSEKKANKPKQNGCGCC 111
Ubl_MUBs_plant cd01814
ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); ...
 5-47 4.56e-05

ubiquitin-like (Ubl) domain found in plant membrane-anchored ubiquitin-fold proteins (MUBs); The plant MUBs belong to a family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. They may serve as docking site to facilitate the association of specific E2s to the plasma membrane. MUBs contain a ubiquitin-like (Ubl) domain with a beta-grasp Ubl fold.


Pssm-ID: 340512  Cd Length: 89  Bit Score: 37.74  E-value: 4.56e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1317840664  5 EEQVSSPNILRLIYQGRFLHGNVTLGALKLPF----GKTTVMHLVAR 47
Cdd:cd01814   41 ENGPKSINDVKLIYAGKVLENGKTLADSRTPGkvppGGVITMHVVVR 87
ubiquitin pfam00240
Ubiquitin family; This family contains a number of ubiquitin-like proteins: SUMO (smt3 homolog) ...
 4-44 3.86e-03

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: 32.14  E-value: 3.86e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 1317840664  4 EEEQVSSPNILRLIYQGRFLHGNVTLGALKLPFGKTTVMHL 44
Cdd:pfam00240 29 AEKEGVPPEQQRLIYSGKVLEDDQTLGEYGIEDGSTIHLVL 69
 
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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