Ubiquitin-60S ribosomal protein L40 (UBA52)
The protein contains 128 amino acids for an estimated molecular weight of 14728 Da.
Exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.', 'Component of the 60S subunit of the ribosome. Ribosomal protein L40 is essential for translation of a subset of c (updated: Dec. 11, 2019)
Protein identification was indicated in the following studies:
- 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.
- D'Alessandro and co-workers. (2017) Red blood cell proteomics update: is there more to discover? Blood Transfus. 15(2), 182-187.
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.
This protein is annotated as membranous in Gene Ontology.
(right-click above to access to more options from the contextual menu)
Biological Process
Activation of MAPK activity
Aggrephagy
Amyloid fibril formation
Anaphase-promoting complex-dependent catabolic process
Cellular protein metabolic process
Cellular protein modification process
Cytokine-mediated signaling pathway
Cytoplasmic pattern recognition receptor signaling pathway
Cytoplasmic translation
DNA damage response, detection of DNA damage
Endoplasmic reticulum mannose trimming
Endosomal transport
Error-free translesion synthesis
Error-prone translesion synthesis
Global genome nucleotide-excision repair
I-kappaB kinase/NF-kappaB signaling
Interleukin-1-mediated signaling pathway
Interstrand cross-link repair
Intracellular transport of virus
JNK cascade
Membrane organization
Modification-dependent protein catabolic process
Modulation by symbiont of host defense response
MyD88-dependent toll-like receptor signaling pathway
MyD88-independent toll-like receptor signaling pathway
Negative regulation of apoptotic process
Negative regulation of transcription by RNA polymerase II
Negative regulation of transforming growth factor beta receptor signaling pathway
Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
Nucleotide-binding oligomerization domain containing signaling pathway
Nucleotide-excision repair, DNA damage recognition
Nucleotide-excision repair, DNA duplex unwinding
Nucleotide-excision repair, DNA gap filling
Nucleotide-excision repair, DNA incision
Nucleotide-excision repair, DNA incision, 5'-to lesion
Nucleotide-excision repair, preincision complex assembly
Positive regulation of apoptotic process
Positive regulation of NF-kappaB transcription factor activity
Positive regulation of transcription by RNA polymerase II
Pre-replicative complex assembly
Protein deubiquitination
Protein localization
Protein polyubiquitination
Protein targeting to peroxisome
Protein ubiquitination
Regulation of exit from mitosis
Regulation of mRNA stability
Regulation of transcription from RNA polymerase II promoter in response to hypoxia
Response to insecticide
RRNA processing
SRP-dependent cotranslational protein targeting to membrane
Stress-activated MAPK cascade
Transcription-coupled nucleotide-excision repair
Transforming growth factor beta receptor signaling pathway
Translation
Translational initiation
Translesion synthesis
Transmembrane transport
TRIF-dependent toll-like receptor signaling pathway
Viral life cycle
Viral transcription
Viral translation
Virion assembly
Wnt signaling pathway
Cellular Component
Cytoplasm
Cytosol
Cytosolic large ribosomal subunit
Cytosolic ribosome
Cytosolic small ribosomal subunit
Endocytic vesicle membrane
Endoplasmic reticulum
Endoplasmic reticulum membrane
Endoplasmic reticulum quality control compartment
Endosome membrane
Extracellular exosome
Extracellular space
Host cell
Lysosomal membrane
Mitochondrial outer membrane
Nucleoplasm
Nucleus
Plasma membrane
Small ribosomal subunit
Synapse
Vesicle
The reference OMIM entry for this protein is 191321
Ubiquitin a-52-residue ribosomal protein fusion product; uba52
Human ubiquitin carboxyl extension protein, 52-residue; hubcep52
Ubcep, 52-amino acid; cep52
Ribosomal protein l40; rpl40
DESCRIPTION
Ubiquitin is a small protein of 76 amino acids that is found exclusively in eukaryotes and shows extreme evolutionary conservation. Comparison of ubiquitin sequences from species ranging from yeast to human shows that 71 of the 76 residues are conserved. The human genome contains multiple ubiquitin genes, many of which are nonfunctional reverse-transcribed pseudogenes. The transcriptionally active genes generate mRNAs of approximately 600, 1,000, and 2,500 nucleotides, and these have been termed UBA, UBB (191339), and UBC (191340), respectively. The 600-nucleotide UBA transcripts encode human ubiquitin-ribosomal protein fusion proteins and represent products of the UBA52 gene (Baker and Board, 1991) and the UBA80 gene (191343; Lund et al., 1985).CLONING
By screening a placental cDNA library with the tail-like region of the EHD5 pseudogene as probe, Baker and Board (1991) isolated a cDNA encoding a ubiquitin moiety followed by a 52-amino acid tail, which they termed UBA52. UBA52 is 81% identical to yeast Ubi1/Ubi2 and shares conserved cysteine residues. Northern blot analysis revealed expression in lymphocytes and placenta.GENE STRUCTURE
By genomic sequence analysis, Baker and Board (1991) determined that the UBA52 gene contains 5 exons and spans more than 2 kb. The promoter is located in a CpG-rich island, has SP1-binding sites, and lacks a TATA motif, suggesting a structurally typical ribosomal protein gene.MAPPING
Because of the relatively large number of ubiquitin pseudogenes, special strategies are necessary to map the functional genes. Webb et al. (1994) used an intron sequence to localize the UBA52 ubiquitin-ribosomal protein fusion gene. Analysis of somatic cell hybrids containing individual human chromosomes indicated that the UBA52 gene is located on chromosome 19. In situ hybridization studies confirmed the chromosomal localization but showed 2 peaks of hybridization: a major one over 19p13.1-p12 and a secondary one over 19q12-q13.11. Since the peak of hybridization over the short arm was consistently the strongest in 5 individuals, Webb et al. (1994) considered it likely that this is the localization of the UBA52 gene. ... More on the omim web site
Jan. 22, 2020: Protein entry updated
Automatic update: Entry updated from uniprot information.
Nov. 17, 2018: Protein entry updated
Automatic update: OMIM entry 191321 was added.
Oct. 19, 2018: Additional information
Initial protein addition to the database. This entry was referenced in Bryk and co-workers. (2017).