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Protein

Ubiquitin-60S ribosomal protein L40

Gene

Uba52

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: -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.

Sites

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

GO - Molecular functioni

GO - Biological processi

  • response to insecticide Source: RGD
  • translation Source: InterPro

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-RNO-110312 Translesion synthesis by REV1
R-RNO-110314 Recognition of DNA damage by PCNA-containing replication complex
R-RNO-110320 Translesion Synthesis by POLH
R-RNO-1169091 Activation of NF-kappaB in B cells
R-RNO-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-RNO-1253288 Downregulation of ERBB4 signaling
R-RNO-1295596 Spry regulation of FGF signaling
R-RNO-1358803 Downregulation of ERBB2:ERBB3 signaling
R-RNO-168638 NOD1/2 Signaling Pathway
R-RNO-174048 APC/C:Cdc20 mediated degradation of Cyclin B
R-RNO-174084 Autodegradation of Cdh1 by Cdh1:APC/C
R-RNO-174113 SCF-beta-TrCP mediated degradation of Emi1
R-RNO-174154 APC/C:Cdc20 mediated degradation of Securin
R-RNO-174178 APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
R-RNO-174184 Cdc20:Phospho-APC/C mediated degradation of Cyclin A
R-RNO-179409 APC-Cdc20 mediated degradation of Nek2A
R-RNO-182971 EGFR downregulation
R-RNO-187577 SCF(Skp2)-mediated degradation of p27/p21
R-RNO-195253 Degradation of beta-catenin by the destruction complex
R-RNO-201681 TCF dependent signaling in response to WNT
R-RNO-202424 Downstream TCR signaling
R-RNO-205043 NRIF signals cell death from the nucleus
R-RNO-209543 p75NTR recruits signalling complexes
R-RNO-209560 NF-kB is activated and signals survival
R-RNO-2122948 Activated NOTCH1 Transmits Signal to the Nucleus
R-RNO-2173788 Downregulation of TGF-beta receptor signaling
R-RNO-2173791 TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition)
R-RNO-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-RNO-2173796 SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription
R-RNO-2467813 Separation of Sister Chromatids
R-RNO-2559580 Oxidative Stress Induced Senescence
R-RNO-2559582 Senescence-Associated Secretory Phenotype (SASP)
R-RNO-2559585 Oncogene Induced Senescence
R-RNO-2565942 Regulation of PLK1 Activity at G2/M Transition
R-RNO-2672351 Stimuli-sensing channels
R-RNO-2871837 FCERI mediated NF-kB activation
R-RNO-3134975 Regulation of innate immune responses to cytosolic DNA
R-RNO-3322077 Glycogen synthesis
R-RNO-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-RNO-3769402 Deactivation of the beta-catenin transactivating complex
R-RNO-382556 ABC-family proteins mediated transport
R-RNO-445989 TAK1 activates NFkB by phosphorylation and activation of IKKs complex
R-RNO-450302 activated TAK1 mediates p38 MAPK activation
R-RNO-450321 JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
R-RNO-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-RNO-4608870 Asymmetric localization of PCP proteins
R-RNO-4641257 Degradation of AXIN
R-RNO-4641258 Degradation of DVL
R-RNO-4641263 Regulation of FZD by ubiquitination
R-RNO-5205685 Pink/Parkin Mediated Mitophagy
R-RNO-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-RNO-5357905 Regulation of TNFR1 signaling
R-RNO-5357956 TNFR1-induced NFkappaB signaling pathway
R-RNO-5358346 Hedgehog ligand biogenesis
R-RNO-5607761 Dectin-1 mediated noncanonical NF-kB signaling
R-RNO-5607764 CLEC7A (Dectin-1) signaling
R-RNO-5610780 Degradation of GLI1 by the proteasome
R-RNO-5610785 GLI3 is processed to GLI3R by the proteasome
R-RNO-5632684 Hedgehog 'on' state
R-RNO-5654726 Negative regulation of FGFR1 signaling
R-RNO-5654727 Negative regulation of FGFR2 signaling
R-RNO-5654732 Negative regulation of FGFR3 signaling
R-RNO-5654733 Negative regulation of FGFR4 signaling
R-RNO-5655862 Translesion synthesis by POLK
R-RNO-5656121 Translesion synthesis by POLI
R-RNO-5656169 Termination of translesion DNA synthesis
R-RNO-5668541 TNFR2 non-canonical NF-kB pathway
R-RNO-5675221 Negative regulation of MAPK pathway
R-RNO-5675482 Regulation of necroptotic cell death
R-RNO-5676590 NIK-->noncanonical NF-kB signaling
R-RNO-5684264 MAP3K8 (TPL2)-dependent MAPK1/3 activation
R-RNO-5685942 HDR through Homologous Recombination (HRR)
R-RNO-5687128 MAPK6/MAPK4 signaling
R-RNO-5689603 UCH proteinases
R-RNO-5689877 Josephin domain DUBs
R-RNO-5689880 Ub-specific processing proteases
R-RNO-5689896 Ovarian tumor domain proteases
R-RNO-5689901 Metalloprotease DUBs
R-RNO-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-RNO-5696394 DNA Damage Recognition in GG-NER
R-RNO-5696395 Formation of Incision Complex in GG-NER
R-RNO-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-RNO-5696400 Dual Incision in GG-NER
R-RNO-6781823 Formation of TC-NER Pre-Incision Complex
R-RNO-6782135 Dual incision in TC-NER
R-RNO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-RNO-6783310 Fanconi Anemia Pathway
R-RNO-6804756 Regulation of TP53 Activity through Phosphorylation
R-RNO-6804757 Regulation of TP53 Degradation
R-RNO-6804760 Regulation of TP53 Activity through Methylation
R-RNO-6807004 Negative regulation of MET activity
R-RNO-68827 CDT1 association with the CDC6:ORC:origin complex
R-RNO-68949 Orc1 removal from chromatin
R-RNO-69017 CDK-mediated phosphorylation and removal of Cdc6
R-RNO-69229 Ubiquitin-dependent degradation of Cyclin D1
R-RNO-69231 Cyclin D associated events in G1
R-RNO-69481 G2/M Checkpoints
R-RNO-69541 Stabilization of p53
R-RNO-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-RNO-8849469 PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1
R-RNO-8852276 The role of GTSE1 in G2/M progression after G2 checkpoint
R-RNO-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-RNO-8856825 Cargo recognition for clathrin-mediated endocytosis
R-RNO-8856828 Clathrin-mediated endocytosis
R-RNO-8863795 Downregulation of ERBB2 signaling
R-RNO-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-RNO-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-RNO-8939236 RUNX1 regulates transcription of genes involved in differentiation of HSCs
R-RNO-8939902 Regulation of RUNX2 expression and activity
R-RNO-8941858 Regulation of RUNX3 expression and activity
R-RNO-8948747 Regulation of PTEN localization
R-RNO-8948751 Regulation of PTEN stability and activity
R-RNO-8951664 Neddylation
R-RNO-901032 ER Quality Control Compartment (ERQC)
R-RNO-9010553 Regulation of expression of SLITs and ROBOs
R-RNO-9013507 NOTCH3 Activation and Transmission of Signal to the Nucleus
R-RNO-9020702 Interleukin-1 signaling
R-RNO-9033241 Peroxisomal protein import
R-RNO-912631 Regulation of signaling by CBL
R-RNO-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-RNO-917937 Iron uptake and transport
R-RNO-936440 Negative regulators of DDX58/IFIH1 signaling
R-RNO-937042 IRAK2 mediated activation of TAK1 complex
R-RNO-937072 TRAF6-mediated induction of TAK1 complex within TLR4 complex
R-RNO-975163 IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
R-RNO-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-RNO-983168 Antigen processing: Ubiquitination & Proteasome degradation

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Alternative name(s):
Ubiquitin A-52 residue ribosomal protein fusion product 1
Cleaved into the following 2 chains:
Alternative name(s):
CEP52
Gene namesi
Name:Uba52
Synonyms:Ubcep2
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Chromosome 16

Organism-specific databases

RGDi68344 Uba52

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_00003964391 – 76UbiquitinAdd BLAST76
ChainiPRO_000013875477 – 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)By similarity
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-trimethyllysine1 Publication1

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

PaxDbiP62986
PRIDEiP62986

PTM databases

PhosphoSitePlusiP62986

Expressioni

Gene expression databases

BgeeiENSRNOG00000019974
ExpressionAtlasiP62986 baseline and differential
GenevisibleiP62986 RN

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

BioGridi248983, 1 interactor
STRINGi10116.ENSRNOP00000027073

Structurei

3D structure databases

ProteinModelPortaliP62986
SMRiP62986
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
GeneTreeiENSGT00920000149069
HOVERGENiHBG079132
InParanoidiP62986
KOiK02927
OMAiRKTKCGH
OrthoDBiEOG091G178I
PhylomeDBiP62986
TreeFamiTF352129

Family and domain databases

Gene3Di2.20.28.70, 1 hit
InterProiView protein in InterPro
IPR038587 L40e_sf
IPR001975 Ribosomal_L40e
IPR019956 Ubiquitin
IPR029071 Ubiquitin-like_domsf
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.

P62986-1 [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
X82636 mRNA Translation: CAA57958.1
U25064 mRNA Translation: AAC52495.1
RefSeqiNP_113875.1, NM_031687.3
XP_006252997.1, XM_006252935.1
XP_008769368.1, XM_008771146.2
UniGeneiRn.110618
Rn.4300

Genome annotation databases

EnsembliENSRNOT00000027073; ENSRNOP00000027073; ENSRNOG00000019974
GeneIDi64156
KEGGirno:64156

Similar proteinsi

Entry informationi

Entry nameiRL40_RAT
AccessioniPrimary (citable) accession number: P62986
Secondary accession number(s): P02248
, P02249, P02250, P14793, P62989, Q29120, Q63446, Q91887, Q91888
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 10, 2010
Last modified: June 20, 2018
This is version 109 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

Complete proteome, Direct protein sequencing, Reference proteome

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