Summary: Urm1 (Ubiquitin related modifier)
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Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation . Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily .
Xu J, Zhang J, Wang L, Zhou J, Huang H, Wu J, Zhong Y, Shi Y; , Proc Natl Acad Sci U S A. 2006;103:11625-11630.: Solution structure of Urm1 and its implications for the origin of protein modifiers. PUBMED:16864801 EPMC:16864801
Goehring AS, Rivers DM, Sprague GF Jr; , Mol Biol Cell. 2003;14:4329-4341.: Urmylation: a ubiquitin-like pathway that functions during invasive growth and budding in yeast. PUBMED:14551258 EPMC:14551258
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015221
Ubiquitin related modifier 1 (Urm1) is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like urmylation pathway [PUBMED:16864801]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily [PUBMED:14551258].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Cellular component||cytoplasm (GO:0005737)|
|Biological process||tRNA thio-modification (GO:0034227)|
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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
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Curation and family details
|Seed source:||Pfam-B_16507 (release 20.0)|
|Author:||Mistry J, Wood V|
|Number in seed:||29|
|Number in full:||304|
|Average length of the domain:||94.70 aa|
|Average identity of full alignment:||42 %|
|Average coverage of the sequence by the domain:||89.71 %|
|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:||6|
|Download:||download the raw HMM for this family|
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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 Urm1 domain has been found. There are 6 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.
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