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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.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
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-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-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-69229. Ubiquitin-dependent degradation of Cyclin D1.
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-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:
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
Proteomesi
  • UP000002311 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)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 L40Add BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
Cross-linki63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)By similarity
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.
PRIDEiP0CH08.

2D gel databases

SWISS-2DPAGEP61864.

Expressioni

Gene expression databases

ExpressionAtlasiP0CH08. baseline.

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 interactors.
34844. 64 interactors.

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[»]
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[»]
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 ribosomal protein L40e family.Curated
Contains 1 ubiquitin-like domain.PROSITE-ProRule annotation

Phylogenomic databases

InParanoidiP0CH08.
KOiK02927.
OrthoDBiEOG092C5P9Y.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. 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
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[»]
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[»]
ProteinModelPortaliP0CH08.
SMRiP0CH08.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34225. 147 interactors.
34844. 64 interactors.

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.
OrthoDBiEOG092C5P9Y.

Enzyme and pathway databases

BioCyciYEAST:G3O-31397-MONOMER.
ReactomeiR-SCE-110312. Translesion synthesis by REV1.
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-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-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-69229. Ubiquitin-dependent degradation of Cyclin D1.
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-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.

Miscellaneous databases

PROiP0CH08.

Gene expression databases

ExpressionAtlasiP0CH08. baseline.

Family and domain databases

InterProiIPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
IPR000626. Ubiquitin_dom.
[Graphical view]
PfamiPF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view]
PRINTSiPR00348. UBIQUITIN.
SMARTiSM01377. Ribosomal_L40e. 1 hit.
SM00213. UBQ. 1 hit.
[Graphical view]
SUPFAMiSSF54236. SSF54236. 1 hit.
PROSITEiPS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 30, 2016
This is version 62 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

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 one 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.