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P62987

- RL40_HUMAN

UniProt

P62987 - RL40_HUMAN

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Protein

Ubiquitin-60S ribosomal protein L40

Gene
UBA52, UBCEP2
Organism
Homo sapiens (Human)
Status
Reviewed - 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, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. 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.
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, and especially for cap-dependent translation of vesicular stomatitis virus mRNAs.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei54 – 541Activating enzyme
Sitei68 – 681Essential for function
Binding sitei72 – 721Activating enzyme

GO - Molecular functioni

  1. protein binding Source: BHF-UCL
  2. structural constituent of ribosome Source: InterPro

GO - Biological processi

  1. activation of MAPK activity Source: Reactome
  2. anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process Source: Reactome
  3. antigen processing and presentation of exogenous peptide antigen via MHC class I Source: Reactome
  4. antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent Source: Reactome
  5. antigen processing and presentation of peptide antigen via MHC class I Source: Reactome
  6. apoptotic process Source: Reactome
  7. apoptotic signaling pathway Source: Reactome
  8. carbohydrate metabolic process Source: Reactome
  9. cellular protein metabolic process Source: Reactome
  10. cellular protein modification process Source: ProtInc
  11. cellular response to hypoxia Source: Reactome
  12. cytokine-mediated signaling pathway Source: Reactome
  13. DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest Source: Reactome
  14. DNA repair Source: Reactome
  15. endosomal transport Source: Reactome
  16. epidermal growth factor receptor signaling pathway Source: Reactome
  17. Fc-epsilon receptor signaling pathway Source: Reactome
  18. fibroblast growth factor receptor signaling pathway Source: Reactome
  19. G1/S transition of mitotic cell cycle Source: Reactome
  20. G2/M transition of mitotic cell cycle Source: Reactome
  21. gene expression Source: Reactome
  22. glucose metabolic process Source: Reactome
  23. glycogen biosynthetic process Source: Reactome
  24. I-kappaB kinase/NF-kappaB signaling Source: Reactome
  25. innate immune response Source: Reactome
  26. intracellular transport of virus Source: Reactome
  27. ion transmembrane transport Source: Reactome
  28. JNK cascade Source: Reactome
  29. membrane organization Source: Reactome
  30. mitotic cell cycle Source: Reactome
  31. mRNA metabolic process Source: Reactome
  32. MyD88-dependent toll-like receptor signaling pathway Source: Reactome
  33. MyD88-independent toll-like receptor signaling pathway Source: Reactome
  34. negative regulation of apoptotic process Source: Reactome
  35. negative regulation of epidermal growth factor receptor signaling pathway Source: Reactome
  36. negative regulation of transcription from RNA polymerase II promoter Source: Reactome
  37. negative regulation of transforming growth factor beta receptor signaling pathway Source: Reactome
  38. negative regulation of type I interferon production Source: Reactome
  39. negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle Source: Reactome
  40. neurotrophin TRK receptor signaling pathway Source: Reactome
  41. Notch receptor processing Source: Reactome
  42. Notch signaling pathway Source: Reactome
  43. nuclear-transcribed mRNA catabolic process, nonsense-mediated decay Source: Reactome
  44. nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway Source: Reactome
  45. nucleotide-binding oligomerization domain containing signaling pathway Source: Reactome
  46. positive regulation of apoptotic process Source: Reactome
  47. positive regulation of I-kappaB kinase/NF-kappaB signaling Source: Reactome
  48. positive regulation of NF-kappaB transcription factor activity Source: Reactome
  49. positive regulation of transcription from RNA polymerase II promoter Source: Reactome
  50. positive regulation of type I interferon production Source: Reactome
  51. positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle Source: Reactome
  52. protein polyubiquitination Source: Reactome
  53. regulation of apoptotic process Source: Reactome
  54. regulation of transcription from RNA polymerase II promoter in response to hypoxia Source: Reactome
  55. regulation of type I interferon production Source: Reactome
  56. regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle Source: Reactome
  57. RNA metabolic process Source: Reactome
  58. small molecule metabolic process Source: Reactome
  59. SRP-dependent cotranslational protein targeting to membrane Source: Reactome
  60. stress-activated MAPK cascade Source: Reactome
  61. T cell receptor signaling pathway Source: Reactome
  62. toll-like receptor 10 signaling pathway Source: Reactome
  63. toll-like receptor 2 signaling pathway Source: Reactome
  64. toll-like receptor 3 signaling pathway Source: Reactome
  65. toll-like receptor 4 signaling pathway Source: Reactome
  66. toll-like receptor 5 signaling pathway Source: Reactome
  67. toll-like receptor 9 signaling pathway Source: Reactome
  68. toll-like receptor signaling pathway Source: Reactome
  69. toll-like receptor TLR1:TLR2 signaling pathway Source: Reactome
  70. toll-like receptor TLR6:TLR2 signaling pathway Source: Reactome
  71. transcription, DNA-templated Source: Reactome
  72. transcription initiation from RNA polymerase II promoter Source: Reactome
  73. transforming growth factor beta receptor signaling pathway Source: Reactome
  74. translation Source: UniProtKB
  75. translational elongation Source: Reactome
  76. translational initiation Source: Reactome
  77. translational termination Source: Reactome
  78. transmembrane transport Source: Reactome
  79. TRIF-dependent toll-like receptor signaling pathway Source: Reactome
  80. viral life cycle Source: Reactome
  81. viral process Source: Reactome
  82. viral protein processing Source: Reactome
  83. viral transcription Source: Reactome
  84. virion assembly Source: Reactome
Complete GO annotation...

Keywords - Molecular functioni

Ribonucleoprotein, Ribosomal protein

Enzyme and pathway databases

ReactomeiREACT_111080. Spry regulation of FGF signaling.
REACT_111178. ER-Phagosome pathway.
REACT_111184. Negative regulation of FGFR signaling.
REACT_1156. Orc1 removal from chromatin.
REACT_115662. Downregulation of ERBB2:ERBB3 signaling.
REACT_115755. Signaling by ERBB2.
REACT_115828. Downregulation of ERBB4 signaling.
REACT_115831. ISG15 antiviral mechanism.
REACT_115852. Signaling by constitutively active EGFR.
REACT_115893. Membrane binding and targetting of GAG proteins.
REACT_115902. SRP-dependent cotranslational protein targeting to membrane.
REACT_1181. Association of licensing factors with the pre-replicative complex.
REACT_118614. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_118656. Activation of NF-kappaB in B cells.
REACT_118780. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_120726. TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
REACT_120727. Downregulation of TGF-beta receptor signaling.
REACT_120734. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
REACT_120916. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
REACT_121111. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_1221. CDK-mediated phosphorylation and removal of Cdc6.
REACT_12484. EGFR downregulation.
REACT_12555. Downstream TCR signaling.
REACT_13415. p75NTR recruits signalling complexes.
REACT_13464. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_13643. NRIF signals cell death from the nucleus.
REACT_13696. NF-kB is activated and signals survival.
REACT_1404. Peptide chain elongation.
REACT_150471. Separation of Sister Chromatids.
REACT_160089. Constitutive Signaling by NOTCH1 HD Domain Mutants.
REACT_160189. Stimuli-sensing channels.
REACT_160205. NOTCH2 Activation and Transmission of Signal to the Nucleus.
REACT_160243. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_160254. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_160315. Regulation of PLK1 Activity at G2/M Transition.
REACT_1614. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_163977. Regulation of innate immune responses to cytosolic DNA.
REACT_163994. FCERI mediated NF-kB activation.
REACT_169168. Senescence-Associated Secretory Phenotype (SASP).
REACT_169208. Glycogen synthesis.
REACT_169325. Oncogene Induced Senescence.
REACT_169436. Oxidative Stress Induced Senescence.
REACT_172638. Asymmetric localization of PCP proteins.
REACT_1797. Formation of a pool of free 40S subunits.
REACT_18265. Regulation of the Fanconi anemia pathway.
REACT_18410. Fanconi Anemia pathway.
REACT_1949. CDT1 association with the CDC6:ORC:origin complex.
REACT_1986. Eukaryotic Translation Termination.
REACT_199384. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_200716. regulation of FZD by ubiquitination.
REACT_200731. deactivation of the beta-catenin transactivating complex.
REACT_200766. degradation of AXIN.
REACT_200777. TCF dependent signaling in response to WNT.
REACT_200783. Myoclonic epilepsy of Lafora.
REACT_200841. degradation of DVL.
REACT_20549. Autodegradation of the E3 ubiquitin ligase COP1.
REACT_2085. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_21281. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
REACT_21368. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
REACT_21399. activated TAK1 mediates p38 MAPK activation.
REACT_22442. Interleukin-1 signaling.
REACT_225574. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_23787. Regulation of signaling by CBL.
REACT_24918. IRAK1 recruits IKK complex.
REACT_24941. Circadian Clock.
REACT_25018. IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation.
REACT_25120. TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling.
REACT_25148. Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon.
REACT_25271. Negative regulators of RIG-I/MDA5 signaling.
REACT_25325. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_25351. TRAF6 mediated induction of TAK1 complex.
REACT_25354. IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation.
REACT_25359. RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways.
REACT_25374. IKK complex recruitment mediated by RIP1.
REACT_25380. IRAK2 mediated activation of TAK1 complex.
REACT_27258. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_4. Ubiquitin-dependent degradation of Cyclin D1.
REACT_6359. Budding and maturation of HIV virion.
REACT_6761. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
REACT_6785. Autodegradation of Cdh1 by Cdh1:APC/C.
REACT_6818. Assembly Of The HIV Virion.
REACT_6820. APC/C:Cdc20 mediated degradation of Cyclin B.
REACT_6821. SCF-beta-TrCP mediated degradation of Emi1.
REACT_6871. APC/C:Cdc20 mediated degradation of Securin.
REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75776. NOD1/2 Signaling Pathway.
REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_75842. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_79. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_821. Cyclin D associated events in G1.
REACT_9003. SCF(Skp2)-mediated degradation of p27/p21.
REACT_9031. Vpu mediated degradation of CD4.
REACT_9453. Vif-mediated degradation of APOBEC3G.
REACT_9491. Viral mRNA Translation.

Names & Taxonomyi

Protein namesi
Recommended name:
Ubiquitin-60S ribosomal protein L40
Alternative name(s):
CEP52
Ubiquitin A-52 residue ribosomal protein fusion product 1
Cleaved into the following 2 chains:
Gene namesi
Name:UBA52
Synonyms:UBCEP2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 19

Organism-specific databases

HGNCiHGNC:12458. UBA52.

Subcellular locationi

Chain Ubiquitin : Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytosol Source: Reactome
  2. cytosolic large ribosomal subunit Source: UniProtKB
  3. endocytic vesicle membrane Source: Reactome
  4. endosome membrane Source: Reactome
  5. lysosomal membrane Source: UniProtKB
  6. nucleoplasm Source: Reactome
  7. plasma membrane Source: Reactome
  8. ribosome Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi48 – 481K → R: No effect on HLTF-mediated polyubiquitination of PCNA. 1 Publication
Mutagenesisi63 – 631K → R: Abolishes HLTF-mediated polyubiquitination of PCNA. 1 Publication
Mutagenesisi65 – 651S → A: Prevents phosphorylation in case of mitophagy.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 7676UbiquitinPRO_0000396433Add
BLAST
Chaini77 – 1285260S ribosomal protein L40PRO_0000396434Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei6 – 61N6-acetyllysine; alternate By similarity
Cross-linki6 – 6Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate1 Publication
Cross-linki11 – 11Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Cross-linki27 – 27Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) Inferred
Cross-linki29 – 29Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)1 Publication
Cross-linki33 – 33Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) By similarity
Modified residuei48 – 481N6-acetyllysine; alternate By similarity
Cross-linki48 – 48Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate3 Publications
Cross-linki63 – 63Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)2 Publications
Modified residuei65 – 651Phosphoserine; by PINK1
Cross-linki76 – 76Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)
Modified residuei88 – 881N6-acetyllysine1 Publication
Modified residuei98 – 981N6,N6,N6-trimethyllysine By similarity

Post-translational modificationi

Ubiquitin: Phosphorylated at Ser-65 by PINK1 during mitophagy. Phosphorylated ubiquitin specifically binds and activates parkin (PARK2), triggering mitophagy.

Keywords - PTMi

Acetylation, Isopeptide bond, Methylation, Phosphoprotein, Ubl conjugation

Proteomic databases

MaxQBiP62987.
PaxDbiP62987.
PRIDEiP62987.

PTM databases

PhosphoSiteiP62987.

Expressioni

Gene expression databases

ArrayExpressiP62987.
BgeeiP62987.
CleanExiHS_UBA52.
GenevestigatoriP62987.

Organism-specific databases

HPAiHPA041344.

Interactioni

Subunit structurei

Ribosomal protein L40 is part of the 60S ribosomal subunit By similarity.2 Publications

Protein-protein interaction databases

BioGridi113159. 41 interactions.
IntActiP62987. 13 interactions.
MINTiMINT-1137632.
STRINGi9606.ENSP00000388107.

Structurei

Secondary structure

128
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi1 – 88
Beta strandi11 – 177
Beta strandi19 – 213
Helixi23 – 3412
Helixi38 – 403
Beta strandi41 – 455
Beta strandi48 – 503
Helixi57 – 593
Beta strandi66 – 749

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2LJ5NMR-A1-76[»]
2MBHNMR-A1-76[»]
2MJBNMR-A1-76[»]
2RSUNMR-A1-76[»]
3J3Belectron microscopy5.00m77-128[»]
4HJKX-ray1.78A1-76[»]
4JIOX-ray3.60U1-76[»]
ProteinModelPortaliP62987.
SMRiP62987. Positions 1-128.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1 – 7676Ubiquitin-likeAdd
BLAST

Sequence similaritiesi

In the N-terminal section; belongs to the ubiquitin family.
In the C-terminal section; belongs to the ribosomal protein L40e family.

Phylogenomic databases

eggNOGiCOG5272.
HOVERGENiHBG079132.
InParanoidiP62987.
KOiK02927.
OMAiQKYNCEK.
OrthoDBiEOG7JDR1W.
PhylomeDBiP62987.
TreeFamiTF352129.

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.

P62987-1 [UniParc]FASTAAdd to Basket

« Hide

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL    50
EDGRTLSDYN IQKESTLHLV LRLRGGIIEP SLRQLAQKYN CDKMICRKCY 100
ARLHPRAVNC RKKKCGHTNN LRPKKKVK 128
Length:128
Mass (Da):14,728
Last modified:August 10, 2010 - v2
Checksum:i7BCB602ABEFAD02A
GO

Sequence cautioni

The sequence AAK31162.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56998 mRNA. Translation: CAA40313.1.
X56997 Genomic DNA. Translation: CAA40312.1.
X56999 mRNA. Translation: CAA40314.1.
AF348700 mRNA. Translation: AAK31162.1. Different initiation.
AC005253 Genomic DNA. Translation: AAC25582.1.
Y00361 mRNA. Translation: CAA68439.1.
CCDSiCCDS12382.1.
PIRiS34428. UQHUR.
RefSeqiNP_001029102.1. NM_001033930.1.
NP_003324.1. NM_003333.3.
UniGeneiHs.5308.

Genome annotation databases

EnsembliENST00000430157; ENSP00000396910; ENSG00000221983.
ENST00000442744; ENSP00000388107; ENSG00000221983.
ENST00000595158; ENSP00000471622; ENSG00000221983.
ENST00000595683; ENSP00000470419; ENSG00000221983.
ENST00000596273; ENSP00000471062; ENSG00000221983.
ENST00000596304; ENSP00000472264; ENSG00000221983.
ENST00000597451; ENSP00000473048; ENSG00000221983.
ENST00000598780; ENSP00000472545; ENSG00000221983.
ENST00000599551; ENSP00000470507; ENSG00000221983.
ENST00000599595; ENSP00000471464; ENSG00000221983.
GeneIDi7311.
KEGGihsa:7311.
UCSCiuc002njr.3. human.

Polymorphism databases

DMDMi302393718.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56998 mRNA. Translation: CAA40313.1 .
X56997 Genomic DNA. Translation: CAA40312.1 .
X56999 mRNA. Translation: CAA40314.1 .
AF348700 mRNA. Translation: AAK31162.1 . Different initiation.
AC005253 Genomic DNA. Translation: AAC25582.1 .
Y00361 mRNA. Translation: CAA68439.1 .
CCDSi CCDS12382.1.
PIRi S34428. UQHUR.
RefSeqi NP_001029102.1. NM_001033930.1.
NP_003324.1. NM_003333.3.
UniGenei Hs.5308.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2LJ5 NMR - A 1-76 [» ]
2MBH NMR - A 1-76 [» ]
2MJB NMR - A 1-76 [» ]
2RSU NMR - A 1-76 [» ]
3J3B electron microscopy 5.00 m 77-128 [» ]
4HJK X-ray 1.78 A 1-76 [» ]
4JIO X-ray 3.60 U 1-76 [» ]
ProteinModelPortali P62987.
SMRi P62987. Positions 1-128.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 113159. 41 interactions.
IntActi P62987. 13 interactions.
MINTi MINT-1137632.
STRINGi 9606.ENSP00000388107.

PTM databases

PhosphoSitei P62987.

Polymorphism databases

DMDMi 302393718.

Proteomic databases

MaxQBi P62987.
PaxDbi P62987.
PRIDEi P62987.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000430157 ; ENSP00000396910 ; ENSG00000221983 .
ENST00000442744 ; ENSP00000388107 ; ENSG00000221983 .
ENST00000595158 ; ENSP00000471622 ; ENSG00000221983 .
ENST00000595683 ; ENSP00000470419 ; ENSG00000221983 .
ENST00000596273 ; ENSP00000471062 ; ENSG00000221983 .
ENST00000596304 ; ENSP00000472264 ; ENSG00000221983 .
ENST00000597451 ; ENSP00000473048 ; ENSG00000221983 .
ENST00000598780 ; ENSP00000472545 ; ENSG00000221983 .
ENST00000599551 ; ENSP00000470507 ; ENSG00000221983 .
ENST00000599595 ; ENSP00000471464 ; ENSG00000221983 .
GeneIDi 7311.
KEGGi hsa:7311.
UCSCi uc002njr.3. human.

Organism-specific databases

CTDi 7311.
GeneCardsi GC19P018682.
HGNCi HGNC:12458. UBA52.
HPAi HPA041344.
MIMi 191321. gene.
neXtProti NX_P62987.
GenAtlasi Search...

Phylogenomic databases

eggNOGi COG5272.
HOVERGENi HBG079132.
InParanoidi P62987.
KOi K02927.
OMAi QKYNCEK.
OrthoDBi EOG7JDR1W.
PhylomeDBi P62987.
TreeFami TF352129.

Enzyme and pathway databases

Reactomei REACT_111080. Spry regulation of FGF signaling.
REACT_111178. ER-Phagosome pathway.
REACT_111184. Negative regulation of FGFR signaling.
REACT_1156. Orc1 removal from chromatin.
REACT_115662. Downregulation of ERBB2:ERBB3 signaling.
REACT_115755. Signaling by ERBB2.
REACT_115828. Downregulation of ERBB4 signaling.
REACT_115831. ISG15 antiviral mechanism.
REACT_115852. Signaling by constitutively active EGFR.
REACT_115893. Membrane binding and targetting of GAG proteins.
REACT_115902. SRP-dependent cotranslational protein targeting to membrane.
REACT_1181. Association of licensing factors with the pre-replicative complex.
REACT_118614. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_118656. Activation of NF-kappaB in B cells.
REACT_118780. NOTCH1 Intracellular Domain Regulates Transcription.
REACT_120726. TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
REACT_120727. Downregulation of TGF-beta receptor signaling.
REACT_120734. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
REACT_120916. Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
REACT_121111. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
REACT_1221. CDK-mediated phosphorylation and removal of Cdc6.
REACT_12484. EGFR downregulation.
REACT_12555. Downstream TCR signaling.
REACT_13415. p75NTR recruits signalling complexes.
REACT_13464. Regulation of activated PAK-2p34 by proteasome mediated degradation.
REACT_13643. NRIF signals cell death from the nucleus.
REACT_13696. NF-kB is activated and signals survival.
REACT_1404. Peptide chain elongation.
REACT_150471. Separation of Sister Chromatids.
REACT_160089. Constitutive Signaling by NOTCH1 HD Domain Mutants.
REACT_160189. Stimuli-sensing channels.
REACT_160205. NOTCH2 Activation and Transmission of Signal to the Nucleus.
REACT_160243. Constitutive Signaling by NOTCH1 PEST Domain Mutants.
REACT_160254. Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants.
REACT_160315. Regulation of PLK1 Activity at G2/M Transition.
REACT_1614. Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
REACT_163977. Regulation of innate immune responses to cytosolic DNA.
REACT_163994. FCERI mediated NF-kB activation.
REACT_169168. Senescence-Associated Secretory Phenotype (SASP).
REACT_169208. Glycogen synthesis.
REACT_169325. Oncogene Induced Senescence.
REACT_169436. Oxidative Stress Induced Senescence.
REACT_172638. Asymmetric localization of PCP proteins.
REACT_1797. Formation of a pool of free 40S subunits.
REACT_18265. Regulation of the Fanconi anemia pathway.
REACT_18410. Fanconi Anemia pathway.
REACT_1949. CDT1 association with the CDC6:ORC:origin complex.
REACT_1986. Eukaryotic Translation Termination.
REACT_199384. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_200716. regulation of FZD by ubiquitination.
REACT_200731. deactivation of the beta-catenin transactivating complex.
REACT_200766. degradation of AXIN.
REACT_200777. TCF dependent signaling in response to WNT.
REACT_200783. Myoclonic epilepsy of Lafora.
REACT_200841. degradation of DVL.
REACT_20549. Autodegradation of the E3 ubiquitin ligase COP1.
REACT_2085. GTP hydrolysis and joining of the 60S ribosomal subunit.
REACT_21281. TAK1 activates NFkB by phosphorylation and activation of IKKs complex.
REACT_21368. JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1.
REACT_21399. activated TAK1 mediates p38 MAPK activation.
REACT_22442. Interleukin-1 signaling.
REACT_225574. Activated NOTCH1 Transmits Signal to the Nucleus.
REACT_23787. Regulation of signaling by CBL.
REACT_24918. IRAK1 recruits IKK complex.
REACT_24941. Circadian Clock.
REACT_25018. IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation.
REACT_25120. TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling.
REACT_25148. Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon.
REACT_25271. Negative regulators of RIG-I/MDA5 signaling.
REACT_25325. AUF1 (hnRNP D0) destabilizes mRNA.
REACT_25351. TRAF6 mediated induction of TAK1 complex.
REACT_25354. IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation.
REACT_25359. RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways.
REACT_25374. IKK complex recruitment mediated by RIP1.
REACT_25380. IRAK2 mediated activation of TAK1 complex.
REACT_27258. Endosomal Sorting Complex Required For Transport (ESCRT).
REACT_4. Ubiquitin-dependent degradation of Cyclin D1.
REACT_6359. Budding and maturation of HIV virion.
REACT_6761. APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
REACT_6785. Autodegradation of Cdh1 by Cdh1:APC/C.
REACT_6818. Assembly Of The HIV Virion.
REACT_6820. APC/C:Cdc20 mediated degradation of Cyclin B.
REACT_6821. SCF-beta-TrCP mediated degradation of Emi1.
REACT_6871. APC/C:Cdc20 mediated degradation of Securin.
REACT_75768. Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
REACT_75776. NOD1/2 Signaling Pathway.
REACT_75822. Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
REACT_75842. Antigen processing: Ubiquitination & Proteasome degradation.
REACT_79. L13a-mediated translational silencing of Ceruloplasmin expression.
REACT_821. Cyclin D associated events in G1.
REACT_9003. SCF(Skp2)-mediated degradation of p27/p21.
REACT_9031. Vpu mediated degradation of CD4.
REACT_9453. Vif-mediated degradation of APOBEC3G.
REACT_9491. Viral mRNA Translation.

Miscellaneous databases

ChiTaRSi UBA52. human.
GenomeRNAii 7311.
NextBioi 28582.
PROi P62987.
SOURCEi Search...

Gene expression databases

ArrayExpressi P62987.
Bgeei P62987.
CleanExi HS_UBA52.
Genevestigatori P62987.

Family and domain databases

InterProi IPR001975. Ribosomal_L40e.
IPR019956. Ubiquitin.
IPR000626. Ubiquitin-like.
IPR029071. Ubiquitin-rel_dom.
IPR019954. Ubiquitin_CS.
[Graphical view ]
Pfami PF01020. Ribosomal_L40e. 1 hit.
PF00240. ubiquitin. 1 hit.
[Graphical view ]
PRINTSi PR00348. UBIQUITIN.
SMARTi SM00213. UBQ. 1 hit.
[Graphical view ]
SUPFAMi SSF54236. SSF54236. 1 hit.
PROSITEi PS00299. UBIQUITIN_1. 1 hit.
PS50053. UBIQUITIN_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "The human ubiquitin-52 amino acid fusion protein gene shares several structural features with mammalian ribosomal protein genes."
    Baker R.T., Board P.G.
    Nucleic Acids Res. 19:1035-1040(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
    Tissue: Adrenal gland, Lymphocyte and Placenta.
  2. "Human ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52) in salivary epithelial cells."
    Wang H., Zhang Y., Okamoto T.
    Submitted (FEB-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "The DNA sequence and biology of human chromosome 19."
    Grimwood J., Gordon L.A., Olsen A.S., Terry A., Schmutz J., Lamerdin J.E., Hellsten U., Goodstein D., Couronne O., Tran-Gyamfi M., Aerts A., Altherr M., Ashworth L., Bajorek E., Black S., Branscomb E., Caenepeel S., Carrano A.V.
    , Caoile C., Chan Y.M., Christensen M., Cleland C.A., Copeland A., Dalin E., Dehal P., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Garcia C., Georgescu A.M., Glavina T., Gomez M., Gonzales E., Groza M., Hammon N., Hawkins T., Haydu L., Ho I., Huang W., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Larionov V., Leem S.-H., Lopez F., Lou Y., Lowry S., Malfatti S., Martinez D., McCready P.M., Medina C., Morgan J., Nelson K., Nolan M., Ovcharenko I., Pitluck S., Pollard M., Popkie A.P., Predki P., Quan G., Ramirez L., Rash S., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., She X., Smith D., Slezak T., Solovyev V., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wagner M., Wheeler J., Wu K., Xie G., Yang J., Dubchak I., Furey T.S., DeJong P., Dickson M., Gordon D., Eichler E.E., Pennacchio L.A., Richardson P., Stubbs L., Rokhsar D.S., Myers R.M., Rubin E.M., Lucas S.M.
    Nature 428:529-535(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "Molecular conservation of 74 amino acid sequence of ubiquitin between cattle and man."
    Schlesinger D.H., Goldstein G.
    Nature 255:423-424(1975) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-74.
  5. Lubec G., Chen W.-Q., Sun Y.
    Submitted (DEC-2008) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 1-27; 30-42 AND 55-72, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Fetal brain cortex.
  6. "Alzheimer disease-specific conformation of hyperphosphorylated paired helical filament-tau is polyubiquitinated through Lys-48, Lys-11, and Lys-6 ubiquitin conjugation."
    Cripps D., Thomas S.N., Jeng Y., Yang F., Davies P., Yang A.J.
    J. Biol. Chem. 281:10825-10838(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 1-27 AND 43-54, UBIQUITINATION AT LYS-6; LYS-11 AND LYS-48, IDENTIFICATION BY MASS SPECTROMETRY.
  7. "cDNA encoding a human homolog of yeast ubiquitin 1."
    Salvesen G., Lloyd C., Farley D.
    Nucleic Acids Res. 15:5485-5485(1987) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 40-128.
  8. "Differential regulation of EGF receptor internalization and degradation by multiubiquitination within the kinase domain."
    Huang F., Kirkpatrick D., Jiang X., Gygi S.P., Sorkin A.
    Mol. Cell 21:737-748(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, UBIQUITINATION AT LYS-11; LYS-29; LYS-48 AND LYS-63, IDENTIFICATION BY MASS SPECTROMETRY.
  9. "Functional regulation of FEZ1 by the U-box-type ubiquitin ligase E4B contributes to neuritogenesis."
    Okumura F., Hatakeyama S., Matsumoto M., Kamura T., Nakayama K.
    J. Biol. Chem. 279:53533-53543(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-27.
  10. "The proteomic reactor facilitates the analysis of affinity-purified proteins by mass spectrometry: application for identifying ubiquitinated proteins in human cells."
    Vasilescu J., Zweitzig D.R., Denis N.J., Smith J.C., Ethier M., Haines D.S., Figeys D.
    J. Proteome Res. 6:298-305(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION [LARGE SCALE ANALYSIS] AT LYS-48.
    Tissue: Lung adenocarcinoma.
  11. "Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks."
    Motegi A., Liaw H.-J., Lee K.-Y., Roest H.P., Maas A., Wu X., Moinova H., Markowitz S.D., Ding H., Hoeijmakers J.H.J., Myung K.
    Proc. Natl. Acad. Sci. U.S.A. 105:12411-12416(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: UBIQUITINATION AT LYS-63, MUTAGENESIS OF LYS-48 AND LYS-63.
  12. "The emerging complexity of protein ubiquitination."
    Komander D.
    Biochem. Soc. Trans. 37:937-953(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW, FUNCTION.
  13. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-88, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  15. "A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs."
    Lee A.S., Burdeinick-Kerr R., Whelan S.P.
    Proc. Natl. Acad. Sci. U.S.A. 110:324-329(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBUNIT.
  16. Cited for: PHOSPHORYLATION AT SER-65, MUTAGENESIS OF SER-65.
  17. "Determination of structural fluctuations of proteins from structure-based calculations of residual dipolar couplings."
    Montalvao R.W., De Simone A., Vendruscolo M.
    J. Biomol. NMR 53:281-292(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 1-76.
  18. Cited for: STRUCTURE BY ELECTRON MICROSCOPY (5.0 ANGSTROMS) OF 77-128 IN COMPLEX WITHIN THE RIBOSOME, SUBUNIT.

Entry informationi

Entry nameiRL40_HUMAN
AccessioniPrimary (citable) accession number: P62987
Secondary accession number(s): P02248
, P02249, P02250, P14793, P62988, Q29120, Q6LBL4, Q6LDU5, Q8WYN8, Q91887, Q91888, Q9BWD6, Q9BX98, Q9UEF2, Q9UEG1, Q9UEK8, Q9UPK7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 31, 2004
Last sequence update: August 10, 2010
Last modified: September 3, 2014
This is version 99 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Ubiquitin is encoded by 4 different genes. UBA52 and RPS27A genes code for a single copy of ubiquitin fused to the ribosomal proteins L40 and S27a, respectively. UBB and UBC genes code for a polyubiquitin precursor with exact head to tail repeats, the number of repeats differ between species and strains.
For a better understanding, features related to ubiquitin are only indicated for the first chain.

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 19
    Human chromosome 19: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Ribosomal proteins
    Ribosomal proteins families and list of entries
  5. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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