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Protein

Ubiquitin-60S ribosomal protein L40

Gene

ubq-2

Organism
Caenorhabditis elegans
Status
Reviewed-Annotation score: -Protein inferred from homologyi

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-48-linked is involved in protein degradation via the proteasome. 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.By similarity

Miscellaneous

In C.elegans ubiquitin is encoded by 2 different genes. ubq-2 gene codes for a single copy of ubiquitin fused to the ribosomal proteins L40. ubq-1 gene codes for a polyubiquitin precursor with exact head to tail repeats.
For a better understanding, features related to ubiquitin are only indicated for the first chain.

GO - Molecular functioni

  • protein tag Source: GO_Central
  • structural constituent of ribosome Source: InterPro
  • ubiquitin protein ligase binding Source: GO_Central

GO - Biological processi

  • modification-dependent protein catabolic process Source: GO_Central
  • polarity specification of anterior/posterior axis Source: UniProtKB
  • protein ubiquitination Source: GO_Central
  • translation Source: InterPro

Keywordsi

Molecular functionRibonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiR-CEL-110312 Translesion synthesis by REV1
R-CEL-110314 Recognition of DNA damage by PCNA-containing replication complex
R-CEL-110320 Translesion Synthesis by POLH
R-CEL-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-CEL-1253288 Downregulation of ERBB4 signaling
R-CEL-156827 L13a-mediated translational silencing of Ceruloplasmin expression
R-CEL-174113 SCF-beta-TrCP mediated degradation of Emi1
R-CEL-1799339 SRP-dependent cotranslational protein targeting to membrane
R-CEL-182971 EGFR downregulation
R-CEL-195253 Degradation of beta-catenin by the destruction complex
R-CEL-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-CEL-2672351 Stimuli-sensing channels
R-CEL-382556 ABC-family proteins mediated transport
R-CEL-450302 activated TAK1 mediates p38 MAPK activation
R-CEL-450321 JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
R-CEL-4641258 Degradation of DVL
R-CEL-5205685 Pink/Parkin Mediated Mitophagy
R-CEL-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-CEL-5358346 Hedgehog ligand biogenesis
R-CEL-5632684 Hedgehog 'on' state
R-CEL-5654726 Negative regulation of FGFR1 signaling
R-CEL-5654727 Negative regulation of FGFR2 signaling
R-CEL-5654732 Negative regulation of FGFR3 signaling
R-CEL-5654733 Negative regulation of FGFR4 signaling
R-CEL-5675221 Negative regulation of MAPK pathway
R-CEL-5689603 UCH proteinases
R-CEL-5689877 Josephin domain DUBs
R-CEL-5689880 Ub-specific processing proteases
R-CEL-5689896 Ovarian tumor domain proteases
R-CEL-5689901 Metalloprotease DUBs
R-CEL-5696394 DNA Damage Recognition in GG-NER
R-CEL-5696395 Formation of Incision Complex in GG-NER
R-CEL-5696400 Dual Incision in GG-NER
R-CEL-6781823 Formation of TC-NER Pre-Incision Complex
R-CEL-6782135 Dual incision in TC-NER
R-CEL-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-CEL-6807004 Negative regulation of MET activity
R-CEL-68949 Orc1 removal from chromatin
R-CEL-69231 Cyclin D associated events in G1
R-CEL-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-CEL-72689 Formation of a pool of free 40S subunits
R-CEL-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-CEL-8849469 PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1
R-CEL-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-CEL-8856825 Cargo recognition for clathrin-mediated endocytosis
R-CEL-8856828 Clathrin-mediated endocytosis
R-CEL-8863795 Downregulation of ERBB2 signaling
R-CEL-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-CEL-8948747 Regulation of PTEN localization
R-CEL-8948751 Regulation of PTEN stability and activity
R-CEL-901032 ER Quality Control Compartment (ERQC)
R-CEL-9010553 Regulation of expression of SLITs and ROBOs
R-CEL-9020702 Interleukin-1 signaling
R-CEL-912631 Regulation of signaling by CBL
R-CEL-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-CEL-917937 Iron uptake and transport
R-CEL-936440 Negative regulators of DDX58/IFIH1 signaling
R-CEL-937039 IRAK1 recruits IKK complex
R-CEL-937042 IRAK2 mediated activation of TAK1 complex
R-CEL-975144 IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation
R-CEL-975163 IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
R-CEL-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-CEL-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-CEL-983168 Antigen processing: Ubiquitination & Proteasome degradation

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Alternative name(s):
CEP52
Cleaved into the following 2 chains:
Gene namesi
Name:ubq-2
Synonyms:ubib
ORF Names:ZK1010.1
OrganismiCaenorhabditis elegans
Taxonomic identifieri6239 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaNematodaChromadoreaRhabditidaRhabditinaRhabditomorphaRhabditoideaRhabditidaePeloderinaeCaenorhabditis
Proteomesi
  • UP000001940 Componenti: Chromosome III

Organism-specific databases

WormBaseiZK1010.1 ; CE15495 ; WBGene00006728 ; ubq-2

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome 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_00003964441 – 76UbiquitinAdd BLAST76
ChainiPRO_000039644577 – 12860S ribosomal protein L40Add BLAST52

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki48Glycyl 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

EPDiP49632
PaxDbiP49632
PeptideAtlasiP49632
PRIDEiP49632

Expressioni

Gene expression databases

BgeeiWBGene00006728 Expressed in 5 organ(s), highest expression level in multi-cellular organism

Interactioni

Subunit structurei

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi41891, 8 interactors
STRINGi6239.ZK1010.1.1

Structurei

3D structure databases

ProteinModelPortaliP49632
SMRiP49632
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

eggNOGiENOG410IUNU Eukaryota
COG1552 LUCA
GeneTreeiENSGT00930000150893
HOGENOMiHOG000233942
InParanoidiP49632
KOiK02927
OMAiNCQKLIC
OrthoDBiEOG091G178I
PhylomeDBiP49632

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.

P49632-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MQIFVKTLTG KTITLEVEAS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL
60 70 80 90 100
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKQICRKCY
110 120
ARLPPRASNC RKKKCGHSSE LRIKKKLK
Length:128
Mass (Da):14,651
Last modified:August 10, 2010 - v2
Checksum:i00CF9072777F017B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L31492 Genomic DNA Translation: AAC37252.1
Z82083 Genomic DNA Translation: CAB04967.1
PIRiT27638
RefSeqiNP_499695.1, NM_067294.3
UniGeneiCel.8282

Genome annotation databases

EnsemblMetazoaiZK1010.1; ZK1010.1; WBGene00006728
GeneIDi176718
KEGGicel:CELE_ZK1010.1
UCSCiZK1010.1.1 c. elegans

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L31492 Genomic DNA Translation: AAC37252.1
Z82083 Genomic DNA Translation: CAB04967.1
PIRiT27638
RefSeqiNP_499695.1, NM_067294.3
UniGeneiCel.8282

3D structure databases

ProteinModelPortaliP49632
SMRiP49632
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi41891, 8 interactors
STRINGi6239.ZK1010.1.1

Proteomic databases

EPDiP49632
PaxDbiP49632
PeptideAtlasiP49632
PRIDEiP49632

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiZK1010.1; ZK1010.1; WBGene00006728
GeneIDi176718
KEGGicel:CELE_ZK1010.1
UCSCiZK1010.1.1 c. elegans

Organism-specific databases

CTDi176718
WormBaseiZK1010.1 ; CE15495 ; WBGene00006728 ; ubq-2

Phylogenomic databases

eggNOGiENOG410IUNU Eukaryota
COG1552 LUCA
GeneTreeiENSGT00930000150893
HOGENOMiHOG000233942
InParanoidiP49632
KOiK02927
OMAiNCQKLIC
OrthoDBiEOG091G178I
PhylomeDBiP49632

Enzyme and pathway databases

ReactomeiR-CEL-110312 Translesion synthesis by REV1
R-CEL-110314 Recognition of DNA damage by PCNA-containing replication complex
R-CEL-110320 Translesion Synthesis by POLH
R-CEL-1234176 Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
R-CEL-1253288 Downregulation of ERBB4 signaling
R-CEL-156827 L13a-mediated translational silencing of Ceruloplasmin expression
R-CEL-174113 SCF-beta-TrCP mediated degradation of Emi1
R-CEL-1799339 SRP-dependent cotranslational protein targeting to membrane
R-CEL-182971 EGFR downregulation
R-CEL-195253 Degradation of beta-catenin by the destruction complex
R-CEL-2173795 Downregulation of SMAD2/3:SMAD4 transcriptional activity
R-CEL-2672351 Stimuli-sensing channels
R-CEL-382556 ABC-family proteins mediated transport
R-CEL-450302 activated TAK1 mediates p38 MAPK activation
R-CEL-450321 JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
R-CEL-4641258 Degradation of DVL
R-CEL-5205685 Pink/Parkin Mediated Mitophagy
R-CEL-532668 N-glycan trimming in the ER and Calnexin/Calreticulin cycle
R-CEL-5358346 Hedgehog ligand biogenesis
R-CEL-5632684 Hedgehog 'on' state
R-CEL-5654726 Negative regulation of FGFR1 signaling
R-CEL-5654727 Negative regulation of FGFR2 signaling
R-CEL-5654732 Negative regulation of FGFR3 signaling
R-CEL-5654733 Negative regulation of FGFR4 signaling
R-CEL-5675221 Negative regulation of MAPK pathway
R-CEL-5689603 UCH proteinases
R-CEL-5689877 Josephin domain DUBs
R-CEL-5689880 Ub-specific processing proteases
R-CEL-5689896 Ovarian tumor domain proteases
R-CEL-5689901 Metalloprotease DUBs
R-CEL-5696394 DNA Damage Recognition in GG-NER
R-CEL-5696395 Formation of Incision Complex in GG-NER
R-CEL-5696400 Dual Incision in GG-NER
R-CEL-6781823 Formation of TC-NER Pre-Incision Complex
R-CEL-6782135 Dual incision in TC-NER
R-CEL-6782210 Gap-filling DNA repair synthesis and ligation in TC-NER
R-CEL-6807004 Negative regulation of MET activity
R-CEL-68949 Orc1 removal from chromatin
R-CEL-69231 Cyclin D associated events in G1
R-CEL-69601 Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
R-CEL-72689 Formation of a pool of free 40S subunits
R-CEL-72706 GTP hydrolysis and joining of the 60S ribosomal subunit
R-CEL-8849469 PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1
R-CEL-8854050 FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
R-CEL-8856825 Cargo recognition for clathrin-mediated endocytosis
R-CEL-8856828 Clathrin-mediated endocytosis
R-CEL-8863795 Downregulation of ERBB2 signaling
R-CEL-8866652 Synthesis of active ubiquitin: roles of E1 and E2 enzymes
R-CEL-8948747 Regulation of PTEN localization
R-CEL-8948751 Regulation of PTEN stability and activity
R-CEL-901032 ER Quality Control Compartment (ERQC)
R-CEL-9010553 Regulation of expression of SLITs and ROBOs
R-CEL-9020702 Interleukin-1 signaling
R-CEL-912631 Regulation of signaling by CBL
R-CEL-917729 Endosomal Sorting Complex Required For Transport (ESCRT)
R-CEL-917937 Iron uptake and transport
R-CEL-936440 Negative regulators of DDX58/IFIH1 signaling
R-CEL-937039 IRAK1 recruits IKK complex
R-CEL-937042 IRAK2 mediated activation of TAK1 complex
R-CEL-975144 IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation
R-CEL-975163 IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
R-CEL-975956 Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
R-CEL-975957 Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
R-CEL-983168 Antigen processing: Ubiquitination & Proteasome degradation

Miscellaneous databases

PROiPR:P49632

Gene expression databases

BgeeiWBGene00006728 Expressed in 5 organ(s), highest expression level in multi-cellular organism

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
ProtoNetiSearch...

Entry informationi

Entry nameiRL40_CAEEL
AccessioniPrimary (citable) accession number: P49632
Secondary accession number(s): P14792, Q9U1P3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: August 10, 2010
Last modified: November 7, 2018
This is version 113 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programCaenorhabditis annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Ribosomal proteins
    Ribosomal proteins families and list of entries
  3. Caenorhabditis elegans
    Caenorhabditis elegans: entries, gene names and cross-references to WormBase
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Main funding by: National Institutes of Health

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