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Protein

Ubiquitin-60S ribosomal protein L40

Gene

Uba52

Organism
Mus musculus (Mouse)
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.1 Publication
60S ribosomal protein L40: Component of the 60S subunit of the ribosome.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei54 – 541Activating enzyme
Sitei68 – 681Essential for function
Binding sitei72 – 721Activating enzyme

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-MMU-508751. Circadian Clock.

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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componentsi: Chromosome 4, Chromosome 8

Organism-specific databases

MGIiMGI:98887. Uba52.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

  • cytosol Source: Reactome
  • intracellular Source: MGI
  • myelin sheath Source: UniProtKB
  • nucleoplasm Source: Reactome
  • ribosome Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396435Add
BLAST
Chaini77 – 1285260S ribosomal protein L40PRO_0000138752Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Modified residuei65 – 651Phosphoserine; by PINK1By similarity
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei98 – 981N6,N6,N6-trimethyllysineBy similarity

Post-translational modificationi

Ubiquitin: Phosphorylated at Ser-65 by PINK1 during mitophagy. Phosphorylated ubiquitin specifically binds and activates parkin (PARK2), 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

EPDiP62984.
PaxDbiP62984.
PRIDEiP62984.
TopDownProteomicsiP62984.

2D gel databases

REPRODUCTION-2DPAGEP62991.

PTM databases

iPTMnetiP62984.
PhosphoSiteiP62984.
SwissPalmiP62984.

Expressioni

Gene expression databases

BgeeiP62984.
ExpressionAtlasiP62984. baseline and differential.
GenevisibleiP62984. MM.

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

BioGridi204401. 3 interactions.
MINTiMINT-1214732.
STRINGi10090.ENSMUSP00000086852.

Structurei

Secondary structure

128
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 66
Beta strandi12 – 176
Helixi23 – 3412
Helixi38 – 403
Beta strandi42 – 454
Helixi57 – 593
Beta strandi66 – 705

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AI5X-ray1.40A1-74[»]
ProteinModelPortaliP62984.
SMRiP62984. Positions 1-107.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP62984.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-likePROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the ribosomal protein L40e family.Curated
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0003. Eukaryota.
COG1552. LUCA.
COG5272. LUCA.
HOVERGENiHBG079132.
InParanoidiP62984.
KOiK02927.
OrthoDBiEOG7JDR1W.
PhylomeDBiP62984.
TreeFamiTF352129.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

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

P62984-1 [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
AF118402 mRNA. Translation: AAD14688.1.
AK018726 mRNA. Translation: BAB31371.1.
BC054413 mRNA. Translation: AAH54413.1.
CCDSiCCDS22371.1.
PIRiS11248.
RefSeqiNP_063936.1. NM_019883.3.
UniGeneiMm.297372.
Mm.482129.

Genome annotation databases

EnsembliENSMUST00000081940; ENSMUSP00000080608; ENSMUSG00000090137.
ENSMUST00000089430; ENSMUSP00000086852; ENSMUSG00000068240.
ENSMUST00000125184; ENSMUSP00000120096; ENSMUSG00000090137.
ENSMUST00000129909; ENSMUSP00000121149; ENSMUSG00000090137.
ENSMUST00000135446; ENSMUSP00000123562; ENSMUSG00000090137.
ENSMUST00000140679; ENSMUSP00000123263; ENSMUSG00000090137.
ENSMUST00000165126; ENSMUSP00000137461; ENSMUSG00000090137.
GeneIDi22186.
KEGGimmu:22186.
UCSCiuc009mam.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF118402 mRNA. Translation: AAD14688.1.
AK018726 mRNA. Translation: BAB31371.1.
BC054413 mRNA. Translation: AAH54413.1.
CCDSiCCDS22371.1.
PIRiS11248.
RefSeqiNP_063936.1. NM_019883.3.
UniGeneiMm.297372.
Mm.482129.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3AI5X-ray1.40A1-74[»]
ProteinModelPortaliP62984.
SMRiP62984. Positions 1-107.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204401. 3 interactions.
MINTiMINT-1214732.
STRINGi10090.ENSMUSP00000086852.

PTM databases

iPTMnetiP62984.
PhosphoSiteiP62984.
SwissPalmiP62984.

2D gel databases

REPRODUCTION-2DPAGEP62991.

Proteomic databases

EPDiP62984.
PaxDbiP62984.
PRIDEiP62984.
TopDownProteomicsiP62984.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000081940; ENSMUSP00000080608; ENSMUSG00000090137.
ENSMUST00000089430; ENSMUSP00000086852; ENSMUSG00000068240.
ENSMUST00000125184; ENSMUSP00000120096; ENSMUSG00000090137.
ENSMUST00000129909; ENSMUSP00000121149; ENSMUSG00000090137.
ENSMUST00000135446; ENSMUSP00000123562; ENSMUSG00000090137.
ENSMUST00000140679; ENSMUSP00000123263; ENSMUSG00000090137.
ENSMUST00000165126; ENSMUSP00000137461; ENSMUSG00000090137.
GeneIDi22186.
KEGGimmu:22186.
UCSCiuc009mam.1. mouse.

Organism-specific databases

CTDi7311.
MGIiMGI:98887. Uba52.

Phylogenomic databases

eggNOGiKOG0003. Eukaryota.
COG1552. LUCA.
COG5272. LUCA.
HOVERGENiHBG079132.
InParanoidiP62984.
KOiK02927.
OrthoDBiEOG7JDR1W.
PhylomeDBiP62984.
TreeFamiTF352129.

Enzyme and pathway databases

ReactomeiR-MMU-508751. Circadian Clock.

Miscellaneous databases

EvolutionaryTraceiP62984.
NextBioi302153.
PROiP62984.
SOURCEiSearch...

Gene expression databases

BgeeiP62984.
ExpressionAtlasiP62984. baseline and differential.
GenevisibleiP62984. MM.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Molecular identification of a murine ubiquitin/60S ribosomal fusion protein and expression study in mouse kidney."
    Sun L., Wuethrich R.P.
    Biochem. Genet. 37:139-147(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: SJL/J.
    Tissue: Kidney.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Head and Kidney.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J and FVB/N.
    Tissue: Liver and Mammary tumor.
  4. "The emerging complexity of protein ubiquitination."
    Komander D.
    Biochem. Soc. Trans. 37:937-953(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW, FUNCTION.

Entry informationi

Entry nameiRL40_MOUSE
AccessioniPrimary (citable) accession number: P62984
Secondary accession number(s): P02248
, P02249, P02250, P62991, Q29120, Q62317, Q64223, Q8VCH1, Q91887, Q91888, Q9CXY4, Q9CZM0, Q9D1R5, Q9D8D9, Q9ET23, Q9ET24, Q9Z0H9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 10, 2010
Last modified: May 11, 2016
This is version 106 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

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.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.