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Protein

Ubiquitin-60S ribosomal protein L40

Gene

uep1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission 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: component of the 60S subunit of the ribosome.

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.

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-SPO-110312 Translesion synthesis by REV1
R-SPO-110314 Recognition of DNA damage by PCNA-containing replication complex
R-SPO-110320 Translesion Synthesis by POLH
R-SPO-174113 SCF-beta-TrCP mediated degradation of Emi1
R-SPO-382556 ABC-family proteins mediated transport
R-SPO-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-SPO-5632684 Hedgehog 'on' state
R-SPO-5655862 Translesion synthesis by POLK
R-SPO-5656121 Translesion synthesis by POLI
R-SPO-5656169 Termination of translesion DNA synthesis
R-SPO-5689603 UCH proteinases
R-SPO-5689880 Ub-specific processing proteases
R-SPO-5689901 Metalloprotease DUBs
R-SPO-5696395 Formation of Incision Complex in GG-NER
R-SPO-5696397 Gap-filling DNA repair synthesis and ligation in GG-NER
R-SPO-5696400 Dual Incision in GG-NER
R-SPO-6781823 Formation of TC-NER Pre-Incision Complex
R-SPO-6782135 Dual incision in TC-NER
R-SPO-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-SPO-68949 Orc1 removal from chromatin
R-SPO-69017 CDK-mediated phosphorylation and removal of Cdc6
R-SPO-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-SPO-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-SPO-8866654 E3 ubiquitin ligases ubiquitinate target proteins
R-SPO-9033241 Peroxisomal protein import
R-SPO-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-SPO-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:uep1
Synonyms:ubi2
ORF Names:SPAC1805.12c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome I

Organism-specific databases

PomBaseiSPAC1805.12c uep1

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003964521 – 76UbiquitinAdd BLAST76
ChainiPRO_000039645377 – 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)
Cross-linki11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
Cross-linki27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)
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)
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)PROSITE-ProRule annotation

Keywords - PTMi

Isopeptide bond, Ubl conjugation

Proteomic databases

PRIDEiP0CH07

PTM databases

iPTMnetiP0CH07

Interactioni

Subunit structurei

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

Protein-protein interaction databases

BioGridi278262, 5 interactors
278890, 14 interactors

Structurei

Secondary structure

1128
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1 – 7Combined sources7
Beta strandi12 – 18Combined sources7
Helixi23 – 34Combined sources12
Helixi38 – 40Combined sources3
Beta strandi42 – 45Combined sources4
Helixi56 – 59Combined sources4
Beta strandi66 – 70Combined sources5

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4II2X-ray2.20B1-76[»]
4II3X-ray2.90B/D1-76[»]
ProteinModelPortaliP0CH07
SMRiP0CH07
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

InParanoidiP0CH07
KOiK02927
OrthoDBiEOG092C5P9Y
PhylomeDBiP0CH07

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.

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 10, 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

Similar proteinsi

Entry informationi

Entry nameiRL402_SCHPO
AccessioniPrimary (citable) accession number: P0CH07
Secondary accession number(s): O13697
, O14257, P0C014, P0C015, Q76PD0, Q9HDZ4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 10, 2010
Last sequence update: August 10, 2010
Last modified: May 23, 2018
This is version 61 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. 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

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