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Protein

Ubiquitin-60S ribosomal protein L40

Gene

UBA52

Organism
Sus scrofa (Pig)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Ubiquitin: 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 (By similarity).By similarity
60S ribosomal protein L40: Component of the 60S subunit of the ribosome.By similarity

Miscellaneous

Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.
For a better understanding, features related to ubiquitin are only indicated for the first chain.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei54Activating enzyme1
Sitei68Essential for function1
Binding sitei72Activating enzyme1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-SSC-110312. Translesion synthesis by REV1.
R-SSC-110314. Recognition of DNA damage by PCNA-containing replication complex.
R-SSC-110320. Translesion Synthesis by POLH.
R-SSC-1234176. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
R-SSC-1253288. Downregulation of ERBB4 signaling.
R-SSC-1295596. Spry regulation of FGF signaling.
R-SSC-1358803. Downregulation of ERBB2:ERBB3 signaling.
R-SSC-168638. NOD1/2 Signaling Pathway.
R-SSC-174048. APC/C:Cdc20 mediated degradation of Cyclin B.
R-SSC-174084. Autodegradation of Cdh1 by Cdh1:APC/C.
R-SSC-174154. APC/C:Cdc20 mediated degradation of Securin.
R-SSC-174178. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
R-SSC-174184. Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
R-SSC-179409. APC-Cdc20 mediated degradation of Nek2A.
R-SSC-182971. EGFR downregulation.
R-SSC-187577. SCF(Skp2)-mediated degradation of p27/p21.
R-SSC-195253. Degradation of beta-catenin by the destruction complex.
R-SSC-201681. TCF dependent signaling in response to WNT.
R-SSC-202424. Downstream TCR signaling.
R-SSC-209543. p75NTR recruits signalling complexes.
R-SSC-209560. NF-kB is activated and signals survival.
R-SSC-2173788. Downregulation of TGF-beta receptor signaling.
R-SSC-2173791. TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
R-SSC-2173795. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
R-SSC-2173796. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
R-SSC-2467813. Separation of Sister Chromatids.
R-SSC-2559580. Oxidative Stress Induced Senescence.
R-SSC-2559582. Senescence-Associated Secretory Phenotype (SASP).
R-SSC-2559585. Oncogene Induced Senescence.
R-SSC-2672351. Stimuli-sensing channels.
R-SSC-2871837. FCERI mediated NF-kB activation.
R-SSC-3134975. Regulation of innate immune responses to cytosolic DNA.
R-SSC-349425. Autodegradation of the E3 ubiquitin ligase COP1.
R-SSC-3769402. Deactivation of the beta-catenin transactivating complex.
R-SSC-382556. ABC-family proteins mediated transport.
R-SSC-445989. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
R-SSC-446652. Interleukin-1 family signaling.
R-SSC-450302. activated TAK1 mediates p38 MAPK activation.
R-SSC-450321. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
R-SSC-450408. AUF1 (hnRNP D0) binds and destabilizes mRNA.
R-SSC-4641257. Degradation of AXIN.
R-SSC-4641258. Degradation of DVL.
R-SSC-4641263. Regulation of FZD by ubiquitination.
R-SSC-532668. N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
R-SSC-5357905. Regulation of TNFR1 signaling.
R-SSC-5357956. TNFR1-induced NFkappaB signaling pathway.
R-SSC-5358346. Hedgehog ligand biogenesis.
R-SSC-5607761. Dectin-1 mediated noncanonical NF-kB signaling.
R-SSC-5607764. CLEC7A (Dectin-1) signaling.
R-SSC-5632684. Hedgehog 'on' state.
R-SSC-5654726. Negative regulation of FGFR1 signaling.
R-SSC-5654727. Negative regulation of FGFR2 signaling.
R-SSC-5654732. Negative regulation of FGFR3 signaling.
R-SSC-5654733. Negative regulation of FGFR4 signaling.
R-SSC-5655862. Translesion synthesis by POLK.
R-SSC-5656121. Translesion synthesis by POLI.
R-SSC-5656169. Termination of translesion DNA synthesis.
R-SSC-5668541. TNFR2 non-canonical NF-kB pathway.
R-SSC-5675221. Negative regulation of MAPK pathway.
R-SSC-5675482. Regulation of necroptotic cell death.
R-SSC-5676590. NIK-->noncanonical NF-kB signaling.
R-SSC-5685942. HDR through Homologous Recombination (HRR).
R-SSC-5687128. MAPK6/MAPK4 signaling.
R-SSC-5689603. UCH proteinases.
R-SSC-5689877. Josephin domain DUBs.
R-SSC-5689880. Ub-specific processing proteases.
R-SSC-5689896. Ovarian tumor domain proteases.
R-SSC-5689901. Metalloprotease DUBs.
R-SSC-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
R-SSC-5696394. DNA Damage Recognition in GG-NER.
R-SSC-5696395. Formation of Incision Complex in GG-NER.
R-SSC-5696397. Gap-filling DNA repair synthesis and ligation in GG-NER.
R-SSC-5696400. Dual Incision in GG-NER.
R-SSC-6781823. Formation of TC-NER Pre-Incision Complex.
R-SSC-6782135. Dual incision in TC-NER.
R-SSC-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-SSC-6783310. Fanconi Anemia Pathway.
R-SSC-6804756. Regulation of TP53 Activity through Phosphorylation.
R-SSC-6804757. Regulation of TP53 Degradation.
R-SSC-6804760. Regulation of TP53 Activity through Methylation.
R-SSC-6807004. Negative regulation of MET activity.
R-SSC-68827. CDT1 association with the CDC6:ORC:origin complex.
R-SSC-68949. Orc1 removal from chromatin.
R-SSC-69017. CDK-mediated phosphorylation and removal of Cdc6.
R-SSC-69229. Ubiquitin-dependent degradation of Cyclin D1.
R-SSC-69231. Cyclin D associated events in G1.
R-SSC-69298. Association of licensing factors with the pre-replicative complex.
R-SSC-69481. G2/M Checkpoints.
R-SSC-69541. Stabilization of p53.
R-SSC-69601. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
R-SSC-8849469. PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1.
R-SSC-8852276. The role of GTSE1 in G2/M progression after G2 checkpoint.
R-SSC-8854050. FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
R-SSC-8856825. Cargo recognition for clathrin-mediated endocytosis.
R-SSC-8856828. Clathrin-mediated endocytosis.
R-SSC-8863795. Downregulation of ERBB2 signaling.
R-SSC-8866652. Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
R-SSC-8866654. E3 ubiquitin ligases ubiquitinate target proteins.
R-SSC-8939236. RUNX1 regulates transcription of genes involved in differentiation of HSCs.
R-SSC-8941858. Regulation of RUNX3 expression and activity.
R-SSC-8948747. Regulation of PTEN localization.
R-SSC-8948751. Regulation of PTEN stability and activity.
R-SSC-8951664. Neddylation.
R-SSC-912631. Regulation of signaling by CBL.
R-SSC-917937. Iron uptake and transport.
R-SSC-936440. Negative regulators of DDX58/IFIH1 signaling.
R-SSC-937039. IRAK1 recruits IKK complex.
R-SSC-937042. IRAK2 mediated activation of TAK1 complex.
R-SSC-937072. TRAF6 mediated induction of TAK1 complex.
R-SSC-975110. TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling.
R-SSC-975144. IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation.
R-SSC-975163. IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation.
R-SSC-975957. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
R-SSC-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Alternative name(s):
CEP52
Ubiquitin A-52 residue ribosomal protein fusion product 1
Cleaved into the following 2 chains:
Gene namesi
Name:UBA52
Synonyms:UBCEP2
OrganismiSus scrofa (Pig)
Taxonomic identifieri9823 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaSuinaSuidaeSus
Proteomesi
  • UP000008227 Componenti: Chromosome 2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964361 – 76UbiquitinAdd BLAST76
ChainiPRO_000039643777 – 12860S ribosomal protein L40Add BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Curated
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei65Phosphoserine; by PINK1By similarity1
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei98N6,N6,N6-trimethyllysineBy similarity1

Post-translational modificationi

Ubiquitin: Phosphorylated at Ser-65 by PINK1 during mitophagy. Phosphorylated ubiquitin specifically binds and activates parkin (PRKN), triggering mitophagy. Phosphorylation does not affect E1-mediated E2 charging of ubiquitin but affects discharging of E2 enzymes to form polyubiquitin chains. It also affects deubiquitination by deubiquitinase enzymes such as USP30.By similarity

Keywords - PTMi

Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiP63053.
PeptideAtlasiP63053.
PRIDEiP63053.

Expressioni

Gene expression databases

BgeeiENSSSCG00000013907.
GenevisibleiP63053. SS.

Interactioni

Subunit structurei

Ribosomal protein L40 is part of the 60S ribosomal subunit. Interacts with UBQLN1 (via UBA domain).By similarity

Protein-protein interaction databases

STRINGi9823.ENSSSCP00000014787.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3J7Oelectron microscopy3.50m1-128[»]
3J7Pelectron microscopy3.50m1-128[»]
3J7Qelectron microscopy3.40m1-128[»]
3J7Relectron microscopy3.90m1-128[»]
ProteinModelPortaliP63053.
SMRiP63053.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-likePROSITE-ProRule annotationAdd BLAST76

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the eukaryotic ribosomal protein eL40 family.Curated

Phylogenomic databases

eggNOGiKOG0003. Eukaryota.
COG1552. LUCA.
COG5272. LUCA.
GeneTreeiENSGT00870000136502.
HOVERGENiHBG079132.
InParanoidiP63053.
KOiK02927.
OMAiRKTKCGH.
OrthoDBiEOG091G178I.
TreeFamiTF352129.

Family and domain databases

InterProiView protein in InterPro
IPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
PfamiView protein in Pfam
PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
PRINTSiPR00348. UBIQUITIN.
SMARTiView protein in SMART
SM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiView protein in PROSITE
PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P63053-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKMICRKCY
110 120
ARLHPRAVNC RKKKCGHTNN LRPKKKVK
Length:128
Mass (Da):14,728
Last modified:August 10, 2010 - v2
Checksum:i7BCB602ABEFAD02A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U72496 mRNA. Translation: AAB52914.1.
PIRiA29584.
RefSeqiNP_999376.1. NM_214211.1.
XP_005652973.1. XM_005652916.2.
XP_013846724.1. XM_013991270.1.
XP_013846730.1. XM_013991276.1.
UniGeneiSsc.638.

Genome annotation databases

EnsembliENSSSCT00000015193; ENSSSCP00000014787; ENSSSCG00000013907.
GeneIDi397418.
KEGGissc:397418.

Similar proteinsi

Entry informationi

Entry nameiRL40_PIG
AccessioniPrimary (citable) accession number: P63053
Secondary accession number(s): P02248
, P02249, P02250, P62974, Q29120, Q29203, Q29252, Q91887, Q91888, Q95260
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 10, 2010
Last modified: September 27, 2017
This is version 87 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. SIMILARITY comments
    Index of protein domains and families