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Protein

Ubiquitin-60S ribosomal protein L40

Gene

RPL40A

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
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, 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. Ribosomal protein L40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2.1 Publication

GO - Molecular functioni

  • protein tag Source: SGD
  • structural constituent of ribosome Source: SGD

GO - Biological processi

  • cytoplasmic translation Source: SGD
  • protein ubiquitination Source: SGD
  • ribosomal large subunit assembly Source: SGD
  • ribosomal large subunit export from nucleus Source: SGD
  • ribosome biogenesis Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-31397-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_291351. Orc1 removal from chromatin.
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_303262. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_305425. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_316133. Translesion synthesis by REV1.
REACT_326247. Translesion Synthesis by POLH.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_343770. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_346191. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_347103. ER-Phagosome pathway.
REACT_354180. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_357098. Termination of translesion DNA synthesis.
REACT_357697. Translesion synthesis by POLI.
REACT_359959. Translesion synthesis by POLK.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Cleaved into the following 2 chains:
Alternative name(s):
CEP52
Gene namesi
Name:RPL40A
Synonyms:UBI1
Ordered Locus Names:YIL148W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311 Componenti: Chromosome IX

Organism-specific databases

SGDiS000001410. RPL40A.

Subcellular locationi

Ubiquitin :

GO - Cellular componenti

  • cytosolic large ribosomal subunit Source: SGD
  • nucleus Source: UniProtKB-SubCell
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_0000396454Add
BLAST
Chaini77 – 1285260S ribosomal protein L40PRO_0000138775Add
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

MaxQBiP0CH08.
PRIDEiP0CH08.

2D gel databases

SWISS-2DPAGEP61864.

Expressioni

Gene expression databases

ExpressionAtlasiP0CH08. differential.

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).2 Publications

Protein-protein interaction databases

BioGridi34225. 147 interactions.
34844. 63 interactions.

Structurei

Secondary structure

1
128
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi80 – 9011Combined sources
Beta strandi94 – 963Combined sources
Turni97 – 993Combined sources
Turni113 – 1164Combined sources
Beta strandi121 – 1233Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10801-128[»]
3J6Yelectron microscopy6.10801-128[»]
3J77electron microscopy6.20901-128[»]
3J78electron microscopy6.30901-128[»]
4U3MX-ray3.00Q0/q077-128[»]
4U3NX-ray3.20Q0/q077-128[»]
4U3UX-ray2.90Q0/q077-128[»]
4U4NX-ray3.10Q0/q077-128[»]
4U4OX-ray3.60Q0/q077-128[»]
4U4QX-ray3.00Q0/q077-128[»]
4U4RX-ray2.80Q0/q077-128[»]
4U4UX-ray3.00Q0/q077-128[»]
4U4YX-ray3.20Q0/q077-128[»]
4U4ZX-ray3.10Q0/q077-128[»]
4U50X-ray3.20Q0/q077-128[»]
4U51X-ray3.20Q0/q077-128[»]
4U52X-ray3.00Q0/q077-128[»]
4U53X-ray3.30Q0/q077-128[»]
4U55X-ray3.20Q0/q077-128[»]
4U56X-ray3.45Q0/q077-128[»]
4U6FX-ray3.10Q0/q077-128[»]
4V6Ielectron microscopy8.80Bp77-128[»]
4V88X-ray3.00Bm/Dm1-128[»]
4V8Telectron microscopy8.10m1-128[»]
4V8Yelectron microscopy4.30Bm1-128[»]
4V8Zelectron microscopy6.60Bm1-128[»]
ProteinModelPortaliP0CH08.
SMRiP0CH08. Positions 1-76.
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

InParanoidiP0CH08.
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.

P0CH08-1 [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:
EMBLi
GenBanki
DDBJi
Links Updated
X05728 Genomic DNA. Translation: CAA29195.1.
X05729 Genomic DNA. Translation: CAA29196.1.
Z38059 Genomic DNA. Translation: CAA86130.1.
BK006942 Genomic DNA. Translation: DAA08405.1.
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:
EMBLi
GenBanki
DDBJi
Links Updated
X05728 Genomic DNA. Translation: CAA29195.1.
X05729 Genomic DNA. Translation: CAA29196.1.
Z38059 Genomic DNA. Translation: CAA86130.1.
BK006942 Genomic DNA. Translation: DAA08405.1.
PIRiA29456.
RefSeqiNP_012118.1. NM_001179496.1.
NP_013020.3. NM_001179884.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3J6Xelectron microscopy6.10801-128[»]
3J6Yelectron microscopy6.10801-128[»]
3J77electron microscopy6.20901-128[»]
3J78electron microscopy6.30901-128[»]
4U3MX-ray3.00Q0/q077-128[»]
4U3NX-ray3.20Q0/q077-128[»]
4U3UX-ray2.90Q0/q077-128[»]
4U4NX-ray3.10Q0/q077-128[»]
4U4OX-ray3.60Q0/q077-128[»]
4U4QX-ray3.00Q0/q077-128[»]
4U4RX-ray2.80Q0/q077-128[»]
4U4UX-ray3.00Q0/q077-128[»]
4U4YX-ray3.20Q0/q077-128[»]
4U4ZX-ray3.10Q0/q077-128[»]
4U50X-ray3.20Q0/q077-128[»]
4U51X-ray3.20Q0/q077-128[»]
4U52X-ray3.00Q0/q077-128[»]
4U53X-ray3.30Q0/q077-128[»]
4U55X-ray3.20Q0/q077-128[»]
4U56X-ray3.45Q0/q077-128[»]
4U6FX-ray3.10Q0/q077-128[»]
4V6Ielectron microscopy8.80Bp77-128[»]
4V88X-ray3.00Bm/Dm1-128[»]
4V8Telectron microscopy8.10m1-128[»]
4V8Yelectron microscopy4.30Bm1-128[»]
4V8Zelectron microscopy6.60Bm1-128[»]
ProteinModelPortaliP0CH08.
SMRiP0CH08. Positions 1-76.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34225. 147 interactions.
34844. 63 interactions.

2D gel databases

SWISS-2DPAGEP61864.

Proteomic databases

MaxQBiP0CH08.
PRIDEiP0CH08.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

SGDiS000001410. RPL40A.

Phylogenomic databases

InParanoidiP0CH08.
KOiK02927.
OrthoDBiEOG7D5B06.

Enzyme and pathway databases

BioCyciYEAST:G3O-31397-MONOMER.
ReactomeiREACT_290856. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_291351. Orc1 removal from chromatin.
REACT_302067. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_303262. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_305425. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_307259. Formation of a pool of free 40S subunits.
REACT_314339. SRP-dependent cotranslational protein targeting to membrane.
REACT_316133. Translesion synthesis by REV1.
REACT_326247. Translesion Synthesis by POLH.
REACT_332565. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_343353. Peptide chain elongation.
REACT_343770. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_346191. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_346847. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_347103. ER-Phagosome pathway.
REACT_354180. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_357098. Termination of translesion DNA synthesis.
REACT_357697. Translesion synthesis by POLI.
REACT_359959. Translesion synthesis by POLK.

Miscellaneous databases

NextBioi975410.
PROiP0CH08.

Gene expression databases

ExpressionAtlasiP0CH08. differential.

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]
ProtoNetiSearch...

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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 204508 / S288c.
  3. Cited for: GENOME REANNOTATION.
    Strain: ATCC 204508 / S288c.
  4. "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.
  5. "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.
  6. "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).
  7. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS] (L40).
  8. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS] (L40).
  9. Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-6; LYS-11; LYS-27; LYS-29; LYS-33; LYS-48 AND LYS-63.
    Strain: SUB592.
  10. "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.
  11. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. "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].
  13. "A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs."
    Lee A.S., Burdeinick-Kerr R., Whelan S.P.
    Proc. Natl. Acad. Sci. U.S.A. 110:324-329(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  14. "Crystal structure of the eukaryotic ribosome."
    Ben-Shem A., Jenner L., Yusupova G., Yusupov M.
    Science 330:1203-1209(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (4.0 ANGSTROMS) OF 80S RIBOSOME.
  15. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 77-128 WITHIN THE 60S RIBOSOMAL SUBUNIT.
  16. "Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit."
    Greber B.J., Boehringer D., Montellese C., Ban N.
    Nat. Struct. Mol. Biol. 19:1228-1233(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY ELECTRON MICROSCOPY (8.1 ANGSTROMS) OF 77-128 WITHIN THE 60S RIBOSOMAL SUBUNIT.

Entry informationi

Entry nameiRL401_YEAST
AccessioniPrimary (citable) accession number: P0CH08
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: July 22, 2015
This is version 49 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 IX
    Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

External Data

Dasty 3

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 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.