Ubiquitin thioesterase OTU1 (YOD1)
The protein contains 348 amino acids for an estimated molecular weight of 38322 Da.
Hydrolase that can remove conjugated ubiquitin from proteins and participates in endoplasmic reticulum-associated degradation (ERAD) for misfolded lumenal proteins. May act by triming the ubiquitin chain on the associated substrate to facilitate their threading through the VCP/p97 pore. Ubiquitin moieties on substrates may present a steric impediment to the threading process when the substrate is transferred to the VCP pore and threaded through VCP's axial channel. Mediates deubiquitination of 'Lys-27'-, 'Lys-29'- and 'Lys-33'-linked polyubiquitin chains. Also able to hydrolyze 'Lys-11'-linked ubiquitin chains. Cleaves both polyubiquitin and di-ubiquitin. May play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes. May recruit PLAA, UBXN6 and VCP to damaged lysosome membranes decorated with K48-linked ubiquitin chains and remove these chains allowing autophagosome formation (PubMed:27753622). (updated: Nov. 22, 2017)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
- D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
- Chu and co-workers. (2018) Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 180(1), 118-133.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
(right-click above to access to more options from the contextual menu)
Biological Process
Endoplasmic reticulum unfolded protein response
Macroautophagy
Negative regulation of retrograde protein transport, ER to cytosol
Protein deubiquitination
Protein K11-linked deubiquitination
Protein K27-linked deubiquitination
Protein K29-linked deubiquitination
Protein K33-linked deubiquitination
Protein K48-linked deubiquitination
Protein K63-linked deubiquitination
Ubiquitin-dependent ERAD pathway
Molecular Function
Cysteine-type peptidase activity
Deubiquitinase activity
Lys48-specific deubiquitinase activity
Lys63-specific deubiquitinase activity
Metal ion binding
Nucleic acid binding
Thiol-dependent deubiquitinase
Ubiquitin protein ligase binding
Ubiquitin-specific protease activity involved in negative regulation of retrograde protein transport, ER to cytosol
The reference OMIM entry for this protein is 612023
Yod1 otu deubiquitinating enzyme 1, s. cerevisiae, homolog of; yod1
Otu domain-containing protein 2; otud2
Duba8
DESCRIPTION
Deubiquitinating enzymes (DUBs; see 603478) are proteases that specifically cleave ubiquitin (191339) linkages, negating the action of ubiquitin ligases. DUBA8 belongs to a DUB subfamily characterized by an ovarian tumor (OTU) domain.CLONING
Kayagaki et al. (2007) identified ovarian tumor domain (OTU)-containing protein 2 (OTUD2) in a small interfering RNA (siRNA)-based screen for OTU deubiquitinating enzyme (DUB) family members. The 6,265-basepair mRNA contains an open reading frame (ORF) predicting a 348-amino acid protein. In addition to an OTU domain, the protein includes a zinc finger (ZNF) C2H2 domain.MAPPING
The YOD1 gene maps to chromosome 1q32.1 (Kayagaki et al., 2007). ... More on the omim web site
Feb. 10, 2018: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 612023 was added.
Feb. 24, 2016: Protein entry updated
Automatic update: model status changed