Summary: Ubiquitin fold modifier 1 protein
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
Ubiquitin fold modifier 1 protein Provide feedback
This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesised in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous . While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme .
Komatsu M, Chiba T, Tatsumi K, Iemura S, Tanida I, Okazaki N, Ueno T, Kominami E, Natsume T, Tanaka K; , EMBO J. 2004;23:1977-1986.: A novel protein-conjugating system for Ufm1, a ubiquitin-fold modifier. PUBMED:15071506 EPMC:15071506
Sasakawa H, Sakata E, Yamaguchi Y, Komatsu M, Tatsumi K, Kominami E, Tanaka K, Kato K; , Biochem Biophys Res Commun. 2006;343:21-26.: Solution structure and dynamics of Ufm1, a ubiquitin-fold modifier 1. PUBMED:16527251 EPMC:16527251
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR005375
Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, INTERPRO), a ubiquitin-conjugating enzyme (E2, INTERPRO), and a ubiquitin ligase (E3, INTERPRO, INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process [PUBMED:12646216]. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (INTERPRO), SUMO1 (INTERPRO), NEDD8, Rad23 (INTERPRO), Elongin B and Parkin (INTERPRO), the latter being involved in Parkinson's disease [PUBMED:15564047].
Ubiquitin-like molecules (UBLs) can be divided into two subclasses: type-1 UBLs, which ligate to target proteins in a manner similar, but not identical, to the ubiquitylation pathway, such as SUMO, NEDD8, and UCRP/ISG15, and type-2 UBLs (also called UDPs, ubiquitin-domain proteins), which contain ubiquitin-like structure embedded in a variety of different classes of large proteins with apparently distinct functions, such as Rad23, Elongin B, Scythe, Parkin, and HOIL-1.
This entry represents Ufm1 (ubiquitin-fold modifier), which is a ubiquitin-like protein with structural similarities to ubiquitin [PUBMED:10884686, PUBMED:15071506]. Ufm1 is one of a number of ubiquitin-like modifiers that conjugate to target proteins in cells through Uba5 (E1) and Ufc1 (E2). The Ufm1-system is conserved in metazoa and plants, suggesting it has a potential role in multicellular organisms [PUBMED:16527251]. Human Ufm1 is synthesized as a precursor consisting of 85 amino-acid residues. Prior to activation by Uba5, the extra amino acids at the C-terminal region of Ufm1 are removed to expose Gly, which is necessary for conjugation to target molecule(s). C-terminal processing of Ufm1 requires two specific cysteine peptidases (INTERPRO): UfSP1 and UfSP2; both peptidases are also able to release Ufm1 from Ufm1-conjugated cellular proteins. UfSP2 is present in most, if not all, of multi-cellular organisms including plant, nematode, fly, and mammal, whereas UfSP1 is not present in plants and nematodes [PUBMED:17182609].
For further information on ubiquitin, please see Protein of the Month [PUBMED:].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.
The clan contains the following 41 members:APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Author:||Bateman A, Coggill P|
|Number in seed:||2|
|Number in full:||177|
|Average length of the domain:||72.40 aa|
|Average identity of full alignment:||75 %|
|Average coverage of the sequence by the domain:||67.89 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||9|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Ufm1 domain has been found. There are 3 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
Loading structure mapping...