RL40_DROME
ID RL40_DROME Reviewed; 128 AA.
AC P18101; P68198; Q0E8I1; Q9VKW6; Q9VQX7; Q9VZL4;
DT 01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
DT 10-AUG-2010, sequence version 2.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Ubiquitin-60S ribosomal protein L40;
DE AltName: Full=CEP52;
DE Contains:
DE RecName: Full=Ubiquitin;
DE Contains:
DE RecName: Full=60S ribosomal protein L40;
DE Flags: Precursor;
GN Name=RpL40; Synonyms=Ubi-f, UBI-F52; ORFNames=CG2960;
OS Drosophila melanogaster (Fruit fly).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea;
OC Drosophilidae; Drosophila; Sophophora.
OX NCBI_TaxID=7227;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Canton-S; TISSUE=Larva;
RX PubMed=2165256; DOI=10.1093/nar/18.13.3994;
RA Cabrera y Poch H.L., Arribas C., Izquierdo M.;
RT "Sequence of a Drosophila cDNA encoding a ubiquitin gene fusion to a 52-aa
RT ribosomal protein tail.";
RL Nucleic Acids Res. 18:3994-3994(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Canton-S;
RX PubMed=1381584; DOI=10.1042/bj2860281;
RA Cabrera H.L., Barrio R., Arribas C.;
RT "Structure and expression of the Drosophila ubiquitin-52-amino-acid fusion-
RT protein gene.";
RL Biochem. J. 286:281-288(1992).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Berkeley;
RX PubMed=10731132; DOI=10.1126/science.287.5461.2185;
RA Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D.,
RA Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F.,
RA George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N.,
RA Sutton G.G., Wortman J.R., Yandell M.D., Zhang Q., Chen L.X., Brandon R.C.,
RA Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C.,
RA Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A.,
RA An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A.,
RA Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V.,
RA Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J.,
RA Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E.,
RA Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B.,
RA Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I.,
RA Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C.,
RA Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S.,
RA Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M.,
RA Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M.,
RA Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D.,
RA Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F.,
RA Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D.,
RA Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A.,
RA Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C.,
RA McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C.,
RA Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L.,
RA Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R.,
RA Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V.,
RA Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F.,
RA Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J.,
RA Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R.,
RA Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y.,
RA Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T.,
RA Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S.,
RA Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W.,
RA Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M.,
RA Venter J.C.;
RT "The genome sequence of Drosophila melanogaster.";
RL Science 287:2185-2195(2000).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=Berkeley;
RX PubMed=12537572; DOI=10.1186/gb-2002-3-12-research0083;
RA Misra S., Crosby M.A., Mungall C.J., Matthews B.B., Campbell K.S.,
RA Hradecky P., Huang Y., Kaminker J.S., Millburn G.H., Prochnik S.E.,
RA Smith C.D., Tupy J.L., Whitfield E.J., Bayraktaroglu L., Berman B.P.,
RA Bettencourt B.R., Celniker S.E., de Grey A.D.N.J., Drysdale R.A.,
RA Harris N.L., Richter J., Russo S., Schroeder A.J., Shu S.Q., Stapleton M.,
RA Yamada C., Ashburner M., Gelbart W.M., Rubin G.M., Lewis S.E.;
RT "Annotation of the Drosophila melanogaster euchromatic genome: a systematic
RT review.";
RL Genome Biol. 3:RESEARCH0083.1-RESEARCH0083.22(2002).
RN [5]
RP STRUCTURE BY ELECTRON MICROSCOPY (6.0 ANGSTROMS) OF THE 80S RIBOSOME.
RX PubMed=23636399; DOI=10.1038/nature12104;
RA Anger A.M., Armache J.P., Berninghausen O., Habeck M., Subklewe M.,
RA Wilson D.N., Beckmann R.;
RT "Structures of the human and Drosophila 80S ribosome.";
RL Nature 497:80-85(2013).
CC -!- FUNCTION: [Ubiquitin]: Exists either covalently attached to another
CC protein, or free (unanchored). When covalently bound, it is conjugated
CC to target proteins via an isopeptide bond either as a monomer
CC (monoubiquitin), a polymer linked via different Lys residues of the
CC ubiquitin (polyubiquitin chains) or a linear polymer linked via the
CC initiator Met of the ubiquitin (linear polyubiquitin chains).
CC Polyubiquitin chains, when attached to a target protein, have different
CC functions depending on the Lys residue of the ubiquitin that is linked:
CC Lys-48-linked is involved in protein degradation via the proteasome.
CC Linear polymer chains formed via attachment by the initiator Met lead
CC to cell signaling. Ubiquitin is usually conjugated to Lys residues of
CC target proteins, however, in rare cases, conjugation to Cys or Ser
CC residues has been observed. When polyubiquitin is free (unanchored-
CC polyubiquitin), it also has distinct roles, such as in activation of
CC protein kinases, and in signaling (By similarity). {ECO:0000250}.
CC -!- FUNCTION: [60S ribosomal protein L40]: Component of the 60S subunit of
CC the ribosome. {ECO:0000250}.
CC -!- SUBUNIT: 60S ribosomal protein is part of the 60S ribosomal subunit.
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [Ubiquitin]: Cytoplasm {ECO:0000250}. Nucleus
CC {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: [60S ribosomal protein L40]: Cytoplasm
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: In Drosophila ubiquitin is encoded by 3 different genes.
CC RpL40 and RpS27A genes code for a single copy of ubiquitin fused to the
CC ribosomal proteins L40 and S27a, respectively. Ubi-p63E gene codes for
CC a polyubiquitin precursor with 10 exact head to tail repeats.
CC -!- MISCELLANEOUS: For a better understanding, features related to
CC ubiquitin are only indicated for the first chain.
CC -!- SIMILARITY: In the N-terminal section; belongs to the ubiquitin family.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the eukaryotic
CC ribosomal protein eL40 family. {ECO:0000305}.
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DR EMBL; X53059; CAA37227.1; -; mRNA.
DR EMBL; X59943; CAA42568.1; -; Genomic_DNA.
DR EMBL; AE014134; AAF51034.1; -; Genomic_DNA.
DR RefSeq; NP_001260018.1; NM_001273089.2.
DR RefSeq; NP_476776.1; NM_057428.4.
DR PDB; 4V6W; EM; 6.00 A; Cm=77-128.
DR PDB; 6XU6; EM; 3.50 A; Cm=77-128.
DR PDB; 6XU7; EM; 4.90 A; Cm=77-128.
DR PDB; 6XU8; EM; 3.00 A; Cm=77-128.
DR PDBsum; 4V6W; -.
DR PDBsum; 6XU6; -.
DR PDBsum; 6XU7; -.
DR PDBsum; 6XU8; -.
DR AlphaFoldDB; P18101; -.
DR SMR; P18101; -.
DR BioGRID; 59826; 103.
DR IntAct; P18101; 2.
DR STRING; 7227.FBpp0077159; -.
DR PaxDb; P18101; -.
DR PRIDE; P18101; -.
DR DNASU; 33629; -.
DR EnsemblMetazoa; FBtr0077470; FBpp0077159; FBgn0003941.
DR EnsemblMetazoa; FBtr0334787; FBpp0306837; FBgn0003941.
DR GeneID; 33629; -.
DR KEGG; dme:Dmel_CG2960; -.
DR CTD; 33629; -.
DR FlyBase; FBgn0003941; RpL40.
DR VEuPathDB; VectorBase:FBgn0003941; -.
DR eggNOG; KOG0003; Eukaryota.
DR HOGENOM; CLU_010412_3_4_1; -.
DR InParanoid; P18101; -.
DR OMA; AREYNQN; -.
DR OrthoDB; 1536766at2759; -.
DR PhylomeDB; P18101; -.
DR Reactome; R-DME-110312; Translesion synthesis by REV1.
DR Reactome; R-DME-110314; Recognition of DNA damage by PCNA-containing replication complex.
DR Reactome; R-DME-110320; Translesion Synthesis by POLH.
DR Reactome; R-DME-1234176; Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha.
DR Reactome; R-DME-1253288; Downregulation of ERBB4 signaling.
DR Reactome; R-DME-1295596; Spry regulation of FGF signaling.
DR Reactome; R-DME-1358803; Downregulation of ERBB2:ERBB3 signaling.
DR Reactome; R-DME-156827; L13a-mediated translational silencing of Ceruloplasmin expression.
DR Reactome; R-DME-174048; APC/C:Cdc20 mediated degradation of Cyclin B.
DR Reactome; R-DME-174084; Autodegradation of Cdh1 by Cdh1:APC/C.
DR Reactome; R-DME-174113; SCF-beta-TrCP mediated degradation of Emi1.
DR Reactome; R-DME-174154; APC/C:Cdc20 mediated degradation of Securin.
DR Reactome; R-DME-174178; APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1.
DR Reactome; R-DME-174184; Cdc20:Phospho-APC/C mediated degradation of Cyclin A.
DR Reactome; R-DME-179409; APC-Cdc20 mediated degradation of Nek2A.
DR Reactome; R-DME-1799339; SRP-dependent cotranslational protein targeting to membrane.
DR Reactome; R-DME-182971; EGFR downregulation.
DR Reactome; R-DME-187577; SCF(Skp2)-mediated degradation of p27/p21.
DR Reactome; R-DME-195253; Degradation of beta-catenin by the destruction complex.
DR Reactome; R-DME-201681; TCF dependent signaling in response to WNT.
DR Reactome; R-DME-209360; Ubiquitination and proteolysis of phosphorylated CI.
DR Reactome; R-DME-209447; Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY.
DR Reactome; R-DME-209461; Ubiquitination and degradation of phosphorylated ARM.
DR Reactome; R-DME-209560; NF-kB is activated and signals survival.
DR Reactome; R-DME-2122948; Activated NOTCH1 Transmits Signal to the Nucleus.
DR Reactome; R-DME-2173788; Downregulation of TGF-beta receptor signaling.
DR Reactome; R-DME-2173791; TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition).
DR Reactome; R-DME-2173795; Downregulation of SMAD2/3:SMAD4 transcriptional activity.
DR Reactome; R-DME-2467813; Separation of Sister Chromatids.
DR Reactome; R-DME-2559582; Senescence-Associated Secretory Phenotype (SASP).
DR Reactome; R-DME-3769402; Deactivation of the beta-catenin transactivating complex.
DR Reactome; R-DME-382556; ABC-family proteins mediated transport.
DR Reactome; R-DME-432395; Degradation of TIM.
DR Reactome; R-DME-432524; Degradation of PER.
DR Reactome; R-DME-450408; AUF1 (hnRNP D0) binds and destabilizes mRNA.
DR Reactome; R-DME-4608870; Asymmetric localization of PCP proteins.
DR Reactome; R-DME-4641257; Degradation of AXIN.
DR Reactome; R-DME-4641258; Degradation of DVL.
DR Reactome; R-DME-5205685; PINK1-PRKN Mediated Mitophagy.
DR Reactome; R-DME-532668; N-glycan trimming in the ER and Calnexin/Calreticulin cycle.
DR Reactome; R-DME-5358346; Hedgehog ligand biogenesis.
DR Reactome; R-DME-538864; Degradation of CRY.
DR Reactome; R-DME-5607761; Dectin-1 mediated noncanonical NF-kB signaling.
DR Reactome; R-DME-5610780; Degradation of GLI1 by the proteasome.
DR Reactome; R-DME-5610785; GLI3 is processed to GLI3R by the proteasome.
DR Reactome; R-DME-5632684; Hedgehog 'on' state.
DR Reactome; R-DME-5655862; Translesion synthesis by POLK.
DR Reactome; R-DME-5656121; Translesion synthesis by POLI.
DR Reactome; R-DME-5675482; Regulation of necroptotic cell death.
DR Reactome; R-DME-5676590; NIK-->noncanonical NF-kB signaling.
DR Reactome; R-DME-5689603; UCH proteinases.
DR Reactome; R-DME-5689877; Josephin domain DUBs.
DR Reactome; R-DME-5689880; Ub-specific processing proteases.
DR Reactome; R-DME-5689896; Ovarian tumor domain proteases.
DR Reactome; R-DME-5689901; Metalloprotease DUBs.
DR Reactome; R-DME-5696394; DNA Damage Recognition in GG-NER.
DR Reactome; R-DME-5696395; Formation of Incision Complex in GG-NER.
DR Reactome; R-DME-5696400; Dual Incision in GG-NER.
DR Reactome; R-DME-6781823; Formation of TC-NER Pre-Incision Complex.
DR Reactome; R-DME-6782135; Dual incision in TC-NER.
DR Reactome; R-DME-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR Reactome; R-DME-6804757; Regulation of TP53 Degradation.
DR Reactome; R-DME-68867; Assembly of the pre-replicative complex.
DR Reactome; R-DME-68949; Orc1 removal from chromatin.
DR Reactome; R-DME-69017; CDK-mediated phosphorylation and removal of Cdc6.
DR Reactome; R-DME-69231; Cyclin D associated events in G1.
DR Reactome; R-DME-69601; Ubiquitin Mediated Degradation of Phosphorylated Cdc25A.
DR Reactome; R-DME-72689; Formation of a pool of free 40S subunits.
DR Reactome; R-DME-72706; GTP hydrolysis and joining of the 60S ribosomal subunit.
DR Reactome; R-DME-75815; Ubiquitin-dependent degradation of Cyclin D.
DR Reactome; R-DME-8849469; PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1.
DR Reactome; R-DME-8854050; FBXL7 down-regulates AURKA during mitotic entry and in early mitosis.
DR Reactome; R-DME-8856825; Cargo recognition for clathrin-mediated endocytosis.
DR Reactome; R-DME-8856828; Clathrin-mediated endocytosis.
DR Reactome; R-DME-8863795; Downregulation of ERBB2 signaling.
DR Reactome; R-DME-8866652; Synthesis of active ubiquitin: roles of E1 and E2 enzymes.
DR Reactome; R-DME-8866654; E3 ubiquitin ligases ubiquitinate target proteins.
DR Reactome; R-DME-8939236; RUNX1 regulates transcription of genes involved in differentiation of HSCs.
DR Reactome; R-DME-8939902; Regulation of RUNX2 expression and activity.
DR Reactome; R-DME-8941858; Regulation of RUNX3 expression and activity.
DR Reactome; R-DME-8948747; Regulation of PTEN localization.
DR Reactome; R-DME-8948751; Regulation of PTEN stability and activity.
DR Reactome; R-DME-8951664; Neddylation.
DR Reactome; R-DME-901032; ER Quality Control Compartment (ERQC).
DR Reactome; R-DME-9010553; Regulation of expression of SLITs and ROBOs.
DR Reactome; R-DME-9020702; Interleukin-1 signaling.
DR Reactome; R-DME-9033241; Peroxisomal protein import.
DR Reactome; R-DME-912631; Regulation of signaling by CBL.
DR Reactome; R-DME-917729; Endosomal Sorting Complex Required For Transport (ESCRT).
DR Reactome; R-DME-917937; Iron uptake and transport.
DR Reactome; R-DME-9646399; Aggrephagy.
DR Reactome; R-DME-9648002; RAS processing.
DR Reactome; R-DME-9664873; Pexophagy.
DR Reactome; R-DME-9708530; Regulation of BACH1 activity.
DR Reactome; R-DME-9755511; KEAP1-NFE2L2 pathway.
DR Reactome; R-DME-975956; Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC).
DR Reactome; R-DME-975957; Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC).
DR Reactome; R-DME-9762114; GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2.
DR Reactome; R-DME-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR SignaLink; P18101; -.
DR BioGRID-ORCS; 33629; 1 hit in 1 CRISPR screen.
DR ChiTaRS; RpL40; fly.
DR GenomeRNAi; 33629; -.
DR PRO; PR:P18101; -.
DR Proteomes; UP000000803; Chromosome 2L.
DR Bgee; FBgn0003941; Expressed in mouthpart and 25 other tissues.
DR ExpressionAtlas; P18101; baseline and differential.
DR Genevisible; P18101; DM.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0022625; C:cytosolic large ribosomal subunit; IDA:FlyBase.
DR GO; GO:0022627; C:cytosolic small ribosomal subunit; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0031386; F:protein tag; ISS:FlyBase.
DR GO; GO:0003735; F:structural constituent of ribosome; IBA:GO_Central.
DR GO; GO:0031625; F:ubiquitin protein ligase binding; IBA:GO_Central.
DR GO; GO:0002181; P:cytoplasmic translation; TAS:FlyBase.
DR GO; GO:0019941; P:modification-dependent protein catabolic process; IBA:GO_Central.
DR GO; GO:0036211; P:protein modification process; ISS:FlyBase.
DR GO; GO:0016567; P:protein ubiquitination; ISS:FlyBase.
DR GO; GO:0006412; P:translation; TAS:FlyBase.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; ISS:FlyBase.
DR Gene3D; 4.10.1060.50; -; 1.
DR InterPro; IPR038587; L40e_sf.
DR InterPro; IPR001975; Ribosomal_L40e.
DR InterPro; IPR000626; Ubiquitin-like_dom.
DR InterPro; IPR029071; Ubiquitin-like_domsf.
DR InterPro; IPR019954; Ubiquitin_CS.
DR InterPro; IPR019956; Ubiquitin_dom.
DR Pfam; PF01020; Ribosomal_L40e; 1.
DR Pfam; PF00240; ubiquitin; 1.
DR PRINTS; PR00348; UBIQUITIN.
DR SMART; SM01377; Ribosomal_L40e; 1.
DR SMART; SM00213; UBQ; 1.
DR SUPFAM; SSF54236; SSF54236; 1.
DR PROSITE; PS00299; UBIQUITIN_1; 1.
DR PROSITE; PS50053; UBIQUITIN_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Isopeptide bond; Nucleus; Reference proteome;
KW Ribonucleoprotein; Ribosomal protein; Ubl conjugation.
FT CHAIN 1..76
FT /note="Ubiquitin"
FT /id="PRO_0000396442"
FT CHAIN 77..128
FT /note="60S ribosomal protein L40"
FT /id="PRO_0000396443"
FT DOMAIN 1..76
FT /note="Ubiquitin-like"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00214"
FT SITE 54
FT /note="Interacts with activating enzyme"
FT SITE 68
FT /note="Essential for function"
FT SITE 72
FT /note="Interacts with activating enzyme"
FT CROSSLNK 48
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in ubiquitin)"
FT CROSSLNK 76
FT /note="Glycyl lysine isopeptide (Gly-Lys) (interchain with
FT K-? in acceptor proteins)"
SQ SEQUENCE 128 AA; 14729 MW; 7BDE802AA2D249D2 CRC64;
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN
IQKESTLHLV LRLRGGIIEP SLRILAQKYN CDKMICRKCY ARLHPRATNC RKKKCGHTNN
LRPKKKLK
