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Protein

Ubiquitin-60S ribosomal protein L40

Gene

ubi2

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 4 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. structural constituent of ribosome Source: PomBase

GO - Biological processi

  1. cytoplasmic translation Source: PomBase
  2. ribosome biogenesis Source: PomBase
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiREACT_282727. Orc1 removal from chromatin.
REACT_285524. SRP-dependent cotranslational protein targeting to membrane.
REACT_286053. Formation of a pool of free 40S subunits.
REACT_288072. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_294541. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_294969. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_308182. SCF-beta-TrCP mediated degradation of Emi1.
REACT_310263. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_311207. Peptide chain elongation.
REACT_314493. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_320087. Eukaryotic Translation Termination.
REACT_327472. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_329750. ER-Phagosome pathway.
REACT_331986. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_351650. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_353265. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_354178. Hedgehog 'on' state.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Cleaved into the following 2 chains:
Alternative name(s):
CEP52
Gene namesi
Name:ubi2
Synonyms:uep1
ORF Names:SPAC1805.12c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
ProteomesiUP000002485 Componenti: Chromosome I

Organism-specific databases

PomBaseiSPAC1805.12c.

Subcellular locationi

Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytosol Source: PomBase
  2. cytosolic large ribosomal subunit Source: PomBase
  3. nucleolus Source: PomBase
  4. nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396452Add
BLAST
Chaini77 – 1285260S ribosomal protein L40PRO_0000396453Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Interactioni

Subunit structurei

Ribosomal protein L40 is part of the 60S ribosomal subunit.By similarity

Protein-protein interaction databases

BioGridi278262. 5 interactions.
278890. 13 interactions.

Structurei

Secondary structure

128
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 77Combined sources
Beta strandi12 – 187Combined sources
Helixi23 – 3412Combined sources
Helixi38 – 403Combined sources
Beta strandi42 – 454Combined sources
Helixi56 – 594Combined sources
Beta strandi66 – 705Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4II2X-ray2.20B1-76[»]
4II3X-ray2.90B/D1-76[»]
ProteinModelPortaliP0CH07.
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

InParanoidiP0CH07.
KOiK02927.
OrthoDBiEOG7D5B06.
PhylomeDBiP0CH07.

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.

P0CH07-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIFVKTLTG KTITLEVESS DTIDNVKSKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLKALASKYN CEKQICRKCY
110 120
ARLPPRATNC RKKKCGHTNQ LRPKKKLK
Length:128
Mass (Da):14,595
Last modified:August 9, 2010 - v1
Checksum:iA35EA817EFD46D38
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB55853.1.
PIRiT37547.
RefSeqiNP_593923.1. NM_001019352.2.
NP_594398.1. NM_001019821.2.

Genome annotation databases

EnsemblFungiiSPAC11G7.04.1; SPAC11G7.04.1:pep; SPAC11G7.04.
SPAC1805.12c.1; SPAC1805.12c.1:pep; SPAC1805.12c.
GeneIDi2541768.
2542428.
KEGGispo:SPAC11G7.04.
spo:SPAC1805.12c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329670 Genomic DNA. Translation: CAB55853.1.
PIRiT37547.
RefSeqiNP_593923.1. NM_001019352.2.
NP_594398.1. NM_001019821.2.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4II2X-ray2.20B1-76[»]
4II3X-ray2.90B/D1-76[»]
ProteinModelPortaliP0CH07.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi278262. 5 interactions.
278890. 13 interactions.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC11G7.04.1; SPAC11G7.04.1:pep; SPAC11G7.04.
SPAC1805.12c.1; SPAC1805.12c.1:pep; SPAC1805.12c.
GeneIDi2541768.
2542428.
KEGGispo:SPAC11G7.04.
spo:SPAC1805.12c.

Organism-specific databases

PomBaseiSPAC1805.12c.

Phylogenomic databases

InParanoidiP0CH07.
KOiK02927.
OrthoDBiEOG7D5B06.
PhylomeDBiP0CH07.

Enzyme and pathway databases

ReactomeiREACT_282727. Orc1 removal from chromatin.
REACT_285524. SRP-dependent cotranslational protein targeting to membrane.
REACT_286053. Formation of a pool of free 40S subunits.
REACT_288072. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_294541. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_294969. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_308182. SCF-beta-TrCP mediated degradation of Emi1.
REACT_310263. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_311207. Peptide chain elongation.
REACT_314493. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_320087. Eukaryotic Translation Termination.
REACT_327472. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_329750. ER-Phagosome pathway.
REACT_331986. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_351650. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_353265. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_354178. Hedgehog 'on' state.

Miscellaneous databases

NextBioi20802859.
PROiP0CH07.

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

  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.

Entry informationi

Entry nameiRL402_SCHPO
AccessioniPrimary (citable) accession number: P0CH07
Secondary accession number(s): O13697
, O14257, P0C014, P0C015, Q76PD0, Q9HDZ4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 9, 2010
Last sequence update: August 9, 2010
Last modified: March 31, 2015
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 5 different genes. Ubi1 and ubi2 are synthesized as a polyprotein with one copy of ubiquitin fused to ribosomal protein L40. Ubi3 and ubi5 are polyproteins with one copy of ubiquitin fused to ribosomal proteins S27a and s27b respectively. Ubi4 is a polyprotein containing 5 exact head to tail repeats of ubiquitin.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  3. Ribosomal proteins
    Ribosomal proteins families and list of entries
  4. SIMILARITY comments
    Index of protein domains and families

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.