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P0CH09 (RL402_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 33. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Ubiquitin-60S ribosomal protein L40

Cleaved into the following 2 chains:

  1. Ubiquitin
  2. 60S ribosomal protein L40
    Alternative name(s):
    CEP52
Gene names
Name:RPL40B
Synonyms:UBI2
Ordered Locus Names:YKR094C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length128 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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, and DNA-damage responses. 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.

60S ribosomal protein L40: component of the 60S subunit of the ribosome.

Subunit structure

Ribosomal protein L40 is part of the 60S ribosomal subunit. Mature ribosomes consist of a small (40S) and a large (60S) subunit. The 40S subunit contains 32 different proteins (encoded by 56 genes) and 1 molecule of RNA (18S). The 60S subunit contains 46 different proteins (encoded by 81 genes) and 3 molecules of RNA (25S, 5.8S and 5S). Ref.7

Subcellular location

Ubiquitin: Cytoplasm By similarity. Nucleus By similarity Ref.8.

60S ribosomal protein L40: Cytoplasm Ref.8.

Miscellaneous

Ubiquitin is encoded by 4 different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins L40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein S37. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.

The 60S ribosomal protein L40 is present with 40000 molecules/cell in log phase SD medium.

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 7676Ubiquitin
PRO_0000396455
Chain77 – 1285260S ribosomal protein L40
PRO_0000396456

Regions

Domain1 – 7676Ubiquitin-like

Amino acid modifications

Cross-link6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10
Cross-link11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10 Ref.11
Cross-link27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10
Cross-link29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10
Cross-link33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10
Cross-link48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10 Ref.11
Cross-link63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Ref.10 Ref.11
Cross-link76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Experimental info

Mutagenesis291K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6
Mutagenesis481K → R: Deficiency in ubiquitin-protein conjugate formation. Ref.5 Ref.6
Mutagenesis631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. Ref.5 Ref.6

Sequences

Sequence LengthMass (Da)Tools
P0CH09 [UniParc].

Last modified August 10, 2010. Version 1.
Checksum: 84BD137A4B1F7797

FASTA12814,554
        10         20         30         40         50         60 
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN 

        70         80         90        100        110        120 
IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY ARLPPRATNC RKRKCGHTNQ 


LRPKKKLK 

« Hide

References

« Hide 'large scale' references
[1]"The yeast ubiquitin genes: a family of natural gene fusions."
Oezkaynak E., Finley D., Solomon M.J., Varshavsky A.
EMBO J. 6:1429-1439(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The complete sequence of a 15,820 bp segment of Saccharomyces cerevisiae chromosome XI contains the UBI2 and MPL1 genes and three new open reading frames."
Bou G., Esteban P.F., Baladron V., Gonzalez G.A., Cantalejo J.G., Remacha M.A., Jimenez A., del Rey F., Ballesta J.P.G., Revuelta J.L.
Yeast 9:1349-1354(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"Complete DNA sequence of yeast chromosome XI."
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. expand/collapse author list , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"A proteolytic pathway that recognizes ubiquitin as a degradation signal."
Johnson E.S., Ma P.C.M., Ota I.M., Varshavsky A.
J. Biol. Chem. 270:17442-17456(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYS-29; LYS-48 AND LYS-63.
[6]"A ubiquitin mutant with specific defects in DNA repair and multiubiquitination."
Spence J., Sadis S., Haas A.L., Finley D.
Mol. Cell. Biol. 15:1265-1273(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF LYSINE RESIDUES IN UBIQUITIN.
[7]"The list of cytoplasmic ribosomal proteins of Saccharomyces cerevisiae."
Planta R.J., Mager W.H.
Yeast 14:471-477(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NOMENCLATURE, SUBUNIT (L40).
[8]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
[9]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
[10]"A proteomics approach to understanding protein ubiquitination."
Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., Marsischky G., Roelofs J., Finley D., Gygi S.P.
Nat. Biotechnol. 21:921-926(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
Strain: SUB592.
[11]"A subset of membrane-associated proteins is ubiquitinated in response to mutations in the endoplasmic reticulum degradation machinery."
Hitchcock A.L., Auld K., Gygi S.P., Silver P.A.
Proc. Natl. Acad. Sci. U.S.A. 100:12735-12740(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-11; LYS-48 AND LYS-63.
[12]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[13]"Sites of ubiquitin attachment in Saccharomyces cerevisiae."
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X73541 Genomic DNA. Translation: CAA51949.1.
Z28319 Genomic DNA. Translation: CAA82173.1.
BK006944 Genomic DNA. Translation: DAA09244.1.
PIRA29456.
RefSeqNP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

3D structure databases

ProteinModelPortalP0CH09.
SMRP0CH09. Positions 1-74, 77-128.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34225. 157 interactions.
34844. 76 interactions.
MINTMINT-2788967.

2D gel databases

SWISS-2DPAGEP61864.

Proteomic databases

PRIDEP0CH09.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYIL148W; YIL148W; YIL148W.
YKR094C; YKR094C; YKR094C.
GeneID853969.
854658.
KEGGsce:YIL148W.
sce:YKR094C.

Organism-specific databases

SGDS000001802. RPL40B.

Phylogenomic databases

GeneTreeENSGT00750000117491.
KOK02927.
OrthoDBEOG7D5B06.

Enzyme and pathway databases

BioCycYEAST:G3O-32057-MONOMER.

Gene expression databases

GenevestigatorP61864.

Family and domain databases

InterProIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSPR00348. UBIQUITIN.
SMARTSM00213. UBQ. 1 hit.
[Graphical view]
PROSITEPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio975410.

Entry information

Entry nameRL402_YEAST
AccessionPrimary (citable) accession number: P0CH09
Secondary accession number(s): D6VVD9 expand/collapse secondary AC list , P04838, P14796, P61864, Q6LA96
Entry history
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: April 16, 2014
This is version 33 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XI

Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

Ribosomal proteins

Ribosomal proteins families and list of entries