P62984 (RL40_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

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:

1. Ubiquitin
2. 60S ribosomal protein L40
   Alternative name(s):
   CEP52

Gene names

Name:	Uba52
Synonyms:	Ubcep2

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	128 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.5 Ribosomal protein L40 is a component of the 60S subunit of the ribosome. Ref.5
Subunit structure	Ribosomal protein L40 is part of the 60S ribosomal subunit By similarity.
Subcellular location	Ubiquitin: Cytoplasm By similarity. Nucleus By similarity. 60S ribosomal protein L40: Cytoplasm 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.
Sequence similarities	In the N-terminal section; belongs to the ubiquitin family. In the C-terminal section; belongs to the ribosomal protein L40e family. Contains 1 ubiquitin-like domain.

Ontologies

Keywords
Cellular component	Cytoplasm Nucleus
Molecular function	Ribonucleoprotein Ribosomal protein
PTM	Acetylation Isopeptide bond Methylation Phosphoprotein Ubl conjugation
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	translation Inferred from electronic annotation. Source: InterPro
Cellular_component	cytosol Traceable author statement. Source: Reactome cytosolic large ribosomal subunit Inferred from electronic annotation. Source: Compara nucleoplasm Traceable author statement. Source: Reactome
Molecular_function	structural constituent of ribosome Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 76

76

Ubiquitin

PRO_0000396435

Chain

77 – 128

52

60S ribosomal protein L40

PRO_0000138752

Regions

Domain

1 – 76

76

Ubiquitin-like

Sites

Binding site

54

1

Activating enzyme

Binding site

72

1

Activating enzyme

Site

68

1

Essential for function

Amino acid modifications

Modified residue

6

1

N6-acetyllysine; alternate By similarity

Modified residue

48

1

N6-acetyllysine; alternate By similarity

Modified residue

57

1

Phosphoserine Ref.4

Modified residue

65

1

Phosphoserine By similarity

Modified residue

88

1

N6-acetyllysine By similarity

Modified residue

98

1

N6,N6,N6-trimethyllysine By similarity

Cross-link

6

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity

Cross-link

11

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

27

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

29

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

33

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

48

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate By similarity

Cross-link

63

Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity

Cross-link

76

Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

128

Helix Strand Turn

Details...

Beta strand

1 – 6

6

Beta strand

12 – 17

6

Helix

23 – 34

12

Helix

38 – 40

3

Beta strand

42 – 45

4

Helix

57 – 59

3

Beta strand

66 – 70

5

Sequences

	Sequence		Length	Mass (Da)
	P62984 [UniParc]. Last modified August 10, 2010. Version 2. Checksum: 7BCB602ABEFAD02A	FASTA	128	14,728
	10 20 30 40 50 60 MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 70 80 90 100 110 120 IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKMICRKCY ARLHPRAVNC RKKKCGHTNN LRPKKKVK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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. 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]	"Large-scale phosphorylation analysis of mouse liver." Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P. Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-57, MASS SPECTROMETRY. Tissue: Liver.
[5]	"The emerging complexity of protein ubiquitination." Komander D. Biochem. Soc. Trans. 37:937-953(2009) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW, FUNCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF118402 mRNA. Translation: AAD14688.1.
AK018726 mRNA. Translation: BAB31371.1.
BC054413 mRNA. Translation: AAH54413.1.

IPI

IPI00138892.

PIR

S11248.

RefSeq

NP_063936.1. NM_019883.3.

UniGene

Mm.297372.
Mm.482129.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3AI5	X-ray	1.40	A	1-74	[»]

ProteinModelPortal

P62984.

SMR

P62984. Positions 1-76, 89-128.

ModBase

Search...

PTM databases

PhosphoSite

P62984.

2D gel databases

REPRODUCTION-2DPAGE

P62991.

Proteomic databases

PaxDb

P62984.

PRIDE

P62984.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENSMUST00000081940; ENSMUSP00000080608; ENSMUSG00000090137.
ENSMUST00000089430; ENSMUSP00000086852; ENSMUSG00000068240.
ENSMUST00000125184; ENSMUSP00000120096; ENSMUSG00000090137.
ENSMUST00000129909; ENSMUSP00000121149; ENSMUSG00000090137.
ENSMUST00000135446; ENSMUSP00000123562; ENSMUSG00000090137.
ENSMUST00000140679; ENSMUSP00000123263; ENSMUSG00000090137.
ENSMUST00000165126; ENSMUSP00000137461; ENSMUSG00000090137.

GeneID

22186.

KEGG

mmu:22186.

Organism-specific databases

CTD

7311.

MGI

MGI:98887. Uba52.

Phylogenomic databases

eggNOG

COG5272.

HOVERGEN

HBG079132.

InParanoid

P62984.

KO

K02927.

OrthoDB

EOG4V1726.

Enzyme and pathway databases

Reactome

REACT_109335. Circadian Clock.
REACT_115202. Signal Transduction.
REACT_24972. Circadian Clock (mouse).

Gene expression databases

ArrayExpress

P62984.

Bgee

P62984.

Genevestigator

P62984.

GermOnline

ENSMUSG00000008348. Mus musculus.
ENSMUSG00000019505. Mus musculus.
ENSMUSG00000020460. Mus musculus.
ENSMUSG00000044285. Mus musculus.
ENSMUSG00000058838. Mus musculus.
ENSMUSG00000061390. Mus musculus.
ENSMUSG00000063789. Mus musculus.
ENSMUSG00000066901. Mus musculus.

Family and domain databases

InterPro

IPR001975. Ribosomal_L40e.
IPR000626. Ubiquitin.
IPR019954. Ubiquitin_CS.
IPR019956. Ubiquitin_subgr.
IPR019955. Ubiquitin_supergroup.
[Graphical view]

Pfam

PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]

PRINTS

PR00348. UBIQUITIN.

SMART

SM00213. UBQ. 1 hit.
[Graphical view]

PROSITE

PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P62984.

NextBio

302153.

SOURCE

Search...

Entry information

Entry name

RL40_MOUSE

Accession

Primary (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 history

Integrated into UniProtKB/Swiss-Prot:	August 31, 2004
Last sequence update:	August 10, 2010
Last modified:	April 3, 2013
This is version 74 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program