Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.

P0CH09

- RL402_YEAST

UniProt

P0CH09 - RL402_YEAST

(max 400 entries)x

Your basket is currently empty.

Select item(s) and click on "Add to basket" to create your own collection here
(400 entries max)

Protein

Ubiquitin-60S ribosomal protein L40

Gene

RPL40B

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - 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, 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).By similarity
60S ribosomal protein L40: component of the 60S subunit of the ribosome.

GO - Molecular functioni

  1. protein tag Source: SGD
  2. structural constituent of ribosome Source: SGD

GO - Biological processi

  1. cytoplasmic translation Source: SGD
  2. protein ubiquitination Source: SGD
  3. ribosomal large subunit assembly Source: SGD
  4. ribosomal large subunit export from nucleus Source: SGD
  5. ribosome biogenesis Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-32057-MONOMER.
ReactomeiREACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
REACT_189025. ER-Phagosome pathway.
REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_189189. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_217188. Formation of a pool of free 40S subunits.
REACT_83036. Orc1 removal from chromatin.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Cleaved into the following 2 chains:
Alternative name(s):
CEP52
Gene namesi
Name:RPL40B
Synonyms:UBI2
Ordered Locus Names:YKR094C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome XI

Organism-specific databases

SGDiS000001802. RPL40B.

Subcellular locationi

Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytosolic large ribosomal subunit Source: SGD
  2. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi29 – 291K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication
Mutagenesisi48 – 481K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication
Mutagenesisi63 – 631K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396455Add
BLAST
Chaini77 – 1285260S ribosomal protein L40PRO_0000396456Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PRIDEiP0CH09.

2D gel databases

SWISS-2DPAGEP61864.

Expressioni

Gene expression databases

GenevestigatoriP61864.

Interactioni

Subunit structurei

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).1 Publication

Protein-protein interaction databases

BioGridi34225. 146 interactions.
34844. 63 interactions.
MINTiMINT-2788967.

Structurei

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4CUWelectron microscopy3.70m1-128[»]
ProteinModelPortaliP0CH09.
SMRiP0CH09. Positions 1-128.
ModBaseiSearch...
MobiDBiSearch...

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

GeneTreeiENSGT00760000119338.
InParanoidiP0CH09.
KOiK02927.
OrthoDBiEOG7D5B06.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM00213. 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.

P0CH09 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLKALASKYN CDKSVCRKCY
110 120
ARLPPRATNC RKRKCGHTNQ LRPKKKLK
Length:128
Mass (Da):14,554
Last modified:August 10, 2010 - v1
Checksum:i84BD137A4B1F7797
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73541 Genomic DNA. Translation: CAA51949.1.
Z28319 Genomic DNA. Translation: CAA82173.1.
BK006944 Genomic DNA. Translation: DAA09244.1.
PIRiA29456.
RefSeqiNP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

Genome annotation databases

EnsemblFungiiYIL148W; YIL148W; YIL148W.
YKR094C; YKR094C; YKR094C.
GeneIDi853969.
854658.
KEGGisce:YIL148W.
sce:YKR094C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X73541 Genomic DNA. Translation: CAA51949.1 .
Z28319 Genomic DNA. Translation: CAA82173.1 .
BK006944 Genomic DNA. Translation: DAA09244.1 .
PIRi A29456.
RefSeqi NP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
4CUW electron microscopy 3.70 m 1-128 [» ]
ProteinModelPortali P0CH09.
SMRi P0CH09. Positions 1-128.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 34225. 146 interactions.
34844. 63 interactions.
MINTi MINT-2788967.

2D gel databases

SWISS-2DPAGE P61864.

Proteomic databases

PRIDEi P0CH09.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YIL148W ; YIL148W ; YIL148W .
YKR094C ; YKR094C ; YKR094C .
GeneIDi 853969.
854658.
KEGGi sce:YIL148W.
sce:YKR094C.

Organism-specific databases

SGDi S000001802. RPL40B.

Phylogenomic databases

GeneTreei ENSGT00760000119338.
InParanoidi P0CH09.
KOi K02927.
OrthoDBi EOG7D5B06.

Enzyme and pathway databases

BioCyci YEAST:G3O-32057-MONOMER.
Reactomei REACT_100522. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_188965. SRP-dependent cotranslational protein targeting to membrane.
REACT_189025. ER-Phagosome pathway.
REACT_189050. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_189060. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_189183. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_189189. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_217188. Formation of a pool of free 40S subunits.
REACT_83036. Orc1 removal from chromatin.

Miscellaneous databases

NextBioi 975410.

Gene expression databases

Genevestigatori P61864.

Family and domain databases

InterProi IPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view ]
Pfami PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view ]
PRINTSi PR00348. UBIQUITIN.
SMARTi SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 1 hit.
PROSITEi PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
  9. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
  10. 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. 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].

Entry informationi

Entry nameiRL402_YEAST
AccessioniPrimary (citable) accession number: P0CH09
Secondary accession number(s): D6VVD9
, P04838, P14796, P61864, Q6LA96
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: October 29, 2014
This is version 39 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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.1 Publication

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
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XI
    Yeast (Saccharomyces cerevisiae) chromosome XI: entries and gene names

External Data

Dasty 3