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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: -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-A: Component of the ribosome, a large ribonucleoprotein complex responsible for the synthesis of proteins in the cell. The small ribosomal subunit (SSU) binds messenger RNAs (mRNAs) and translates the encoded message by selecting cognate aminoacyl-transfer RNA (tRNA) molecules. The large subunit (LSU) contains the ribosomal catalytic site termed the peptidyl transferase center (PTC), which catalyzes the formation of peptide bonds, thereby polymerizing the amino acids delivered by tRNAs into a polypeptide chain. The nascent polypeptides leave the ribosome through a tunnel in the LSU and interact with protein factors that function in enzymatic processing, targeting, and the membrane insertion of nascent chains at the exit of the ribosomal tunnel (PubMed:22096102). eL40 is essential for translation of a subset of cellular transcripts, including stress response transcripts, such as DDR2 (PubMed:23169626).1 Publication1 Publication

Miscellaneous

Ubiquitin is encoded by several different genes. UBI1 and UBI2 genes code for a single copy of ubiquitin fused to the ribosomal proteins eL40. UBI3 is a polyprotein with one copy of ubiquitin fused to ribosomal protein eS31. UBI4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.1 Publication
The 60S ribosomal protein L40 is present with 40000 molecules/cell in log phase SD medium.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

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

BioCyciYEAST:G3O-31397-MONOMER
ReactomeiR-SCE-110312 Translesion synthesis by REV1
R-SCE-110314 Recognition of DNA damage by PCNA-containing replication complex
R-SCE-110320 Translesion Synthesis by POLH
R-SCE-156827 L13a-mediated translational silencing of Ceruloplasmin expression
R-SCE-174113 SCF-beta-TrCP mediated degradation of Emi1
R-SCE-1799339 SRP-dependent cotranslational protein targeting to membrane
R-SCE-187577 SCF(Skp2)-mediated degradation of p27/p21
R-SCE-349425 Autodegradation of the E3 ubiquitin ligase COP1
R-SCE-382556 ABC-family proteins mediated transport
R-SCE-450408 AUF1 (hnRNP D0) binds and destabilizes mRNA
R-SCE-5655862 Translesion synthesis by POLK
R-SCE-5656121 Translesion synthesis by POLI
R-SCE-5656169 Termination of translesion DNA synthesis
R-SCE-5675221 Negative regulation of MAPK pathway
R-SCE-5687128 MAPK6/MAPK4 signaling
R-SCE-5689603 UCH proteinases
R-SCE-5689880 Ub-specific processing proteases
R-SCE-5689901 Metalloprotease DUBs
R-SCE-5693565 Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks
R-SCE-5696394 DNA Damage Recognition in GG-NER
R-SCE-5696395 Formation of Incision Complex in GG-NER
R-SCE-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-SCE-5696400 Dual Incision in GG-NER
R-SCE-6781823 Formation of TC-NER Pre-Incision Complex
R-SCE-6782135 Dual incision in TC-NER
R-SCE-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SCE-68949 Orc1 removal from chromatin
R-SCE-69017 CDK-mediated phosphorylation and removal of Cdc6
R-SCE-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-SCE-72689 Formation of a pool of free 40S subunits
R-SCE-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-SCE-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-SCE-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-SCE-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-SCE-9033241 Peroxisomal protein import
R-SCE-917937 Iron uptake and transport
R-SCE-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-SCE-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-SCE-983168 Antigen processing: Ubiquitination & Proteasome degradation

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Cleaved into the following 2 chains:
60S ribosomal protein L40-A1 Publication
Alternative name(s):
CEP52
Large ribosomal subunit protein eL40-A1 Publication
Gene namesi
Name:RPL40A1 Publication
Synonyms:UBI1
Ordered Locus Names:YIL148W
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome IX

Organism-specific databases

SGDiS000001410 RPL40A

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi29K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi48K → R: Deficiency in ubiquitin-protein conjugate formation. 1 Publication1
Mutagenesisi63K → R: Deficiency in ubiquitin-protein conjugate formation. Loss of DNA repair function. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964541 – 76UbiquitinAdd BLAST76
ChainiPRO_000013877577 – 12860S ribosomal protein L40-AAdd BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Cross-linki93Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

MaxQBiP0CH08
PaxDbiP0CH08
PRIDEiP0CH08

2D gel databases

SWISS-2DPAGEiP61864

PTM databases

iPTMnetiP0CH08

Expressioni

Gene expression databases

ExpressionAtlasiP0CH08 differential

Interactioni

Subunit structurei

Component of the large ribosomal subunit (LSU). Mature yeast ribosomes consist of a small (40S) and a large (60S) subunit. The 40S small subunit contains 1 molecule of ribosomal RNA (18S rRNA) and 33 different proteins (encoded by 57 genes). The large 60S subunit contains 3 rRNA molecules (25S, 5.8S and 5S rRNA) and 46 different proteins (encoded by 81 genes) (PubMed:9559554, PubMed:22096102).1 Publication1 Publication

Protein-protein interaction databases

BioGridi34225, 361 interactors
34844, 183 interactors
STRINGi4932.YKR094C

Structurei

Secondary structure

1128
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi80 – 90Combined sources11
Beta strandi94 – 96Combined sources3
Turni97 – 99Combined sources3
Turni113 – 116Combined sources4
Beta strandi121 – 123Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
5APNelectron microscopy3.91m1-128[»]
5APOelectron microscopy3.41m1-128[»]
5DATX-ray3.15Q0/q077-128[»]
5DC3X-ray3.25Q0/q077-128[»]
5DGEX-ray3.45Q0/q077-128[»]
5DGFX-ray3.30Q0/q077-128[»]
5DGVX-ray3.10Q0/q077-128[»]
5FCIX-ray3.40Q0/q077-128[»]
5FCJX-ray3.10Q0/q077-128[»]
5GAKelectron microscopy3.88o1-128[»]
5I4LX-ray3.10Q0/q077-128[»]
5JUOelectron microscopy4.00RA1-128[»]
5JUPelectron microscopy3.50RA1-128[»]
5JUSelectron microscopy4.20RA1-128[»]
5JUTelectron microscopy4.00RA1-128[»]
5JUUelectron microscopy4.00RA1-128[»]
5LYBX-ray3.25Q0/q077-128[»]
5M1Jelectron microscopy3.30m577-128[»]
5MC6electron microscopy3.80AO1-128[»]
5MEIX-ray3.50AN/DO77-128[»]
5NDGX-ray3.70Q0/q077-128[»]
5NDVX-ray3.30Q0/q077-128[»]
5NDWX-ray3.70Q0/q077-128[»]
5OBMX-ray3.40Q0/q077-128[»]
5ON6X-ray3.10AN/DO77-128[»]
5T62electron microscopy3.30z1-128[»]
5T6Relectron microscopy4.50z1-128[»]
5TBWX-ray3.00AN/DO77-128[»]
5TGAX-ray3.30Q0/q077-128[»]
5TGMX-ray3.50Q0/q077-128[»]
ProteinModelPortaliP0CH08
SMRiP0CH08
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1 – 76Ubiquitin-likePROSITE-ProRule annotationAdd BLAST76

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.Curated
In the C-terminal section; belongs to the eukaryotic ribosomal protein eL40 family.Curated

Phylogenomic databases

InParanoidiP0CH08
KOiK02927
OMAiRKTKCGH
OrthoDBiEOG092C5P9Y

Family and domain databases

Gene3Di2.20.28.70, 1 hit
InterProiView protein in InterPro
IPR038587 L40e_sf
IPR001975 Ribosomal_L40e
IPR019956 Ubiquitin
IPR029071 Ubiquitin-like_domsf
IPR019954 Ubiquitin_CS
IPR000626 Ubiquitin_dom
PfamiView protein in Pfam
PF01020 Ribosomal_L40e, 1 hit
PF00240 ubiquitin, 1 hit
PRINTSiPR00348 UBIQUITIN
SMARTiView protein in SMART
SM01377 Ribosomal_L40e, 1 hit
SM00213 UBQ, 1 hit
SUPFAMiSSF54236 SSF54236, 1 hit
PROSITEiView protein in PROSITE
PS00299 UBIQUITIN_1, 1 hit
PS50053 UBIQUITIN_2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiRL40A_YEAST
AccessioniPrimary (citable) accession number: P0CH08
Secondary accession number(s): D6VVD9
, P04838, P14796, P61864, Q6LA96
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: May 23, 2018
This is version 77 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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

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