ELP5_YEAST
ID ELP5_YEAST Reviewed; 309 AA.
AC P38874; D3DLD5;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=Elongator complex protein 5;
DE AltName: Full=Gamma-toxin target 5;
DE AltName: Full=HAT-associated protein 2;
DE AltName: Full=Protein IKI1;
GN Name=IKI1; Synonyms=ELP5, HAP2, TOT5; OrderedLocusNames=YHR187W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9145530; DOI=10.1271/bbb.61.704;
RA Yajima H., Tokunaga M., Nakayama-Murayama A., Hishinuma F.;
RT "Characterization of IKI1 and IKI3 genes conferring pGKL killer sensitivity
RT on Saccharomyces cerevisiae.";
RL Biosci. Biotechnol. Biochem. 61:704-709(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [4]
RP SUBCELLULAR LOCATION.
RX PubMed=10024884; DOI=10.1016/s1097-2765(00)80179-3;
RA Otero G., Fellows J., Li Y., de Bizemont T., Dirac A.M., Gustafsson C.M.,
RA Erdjument-Bromage H., Tempst P., Svejstrup J.Q.;
RT "Elongator, a multisubunit component of a novel RNA polymerase II
RT holoenzyme for transcriptional elongation.";
RL Mol. Cell 3:109-118(1999).
RN [5]
RP FUNCTION OF THE ELONGATOR COMPLEX IN ZYMOCIN SENSITIVITY.
RX PubMed=11296232; DOI=10.1093/emboj/20.8.1993;
RA Frohloff F., Fichtner L., Jablonowski D., Breunig K.D., Schaffrath R.;
RT "Saccharomyces cerevisiae Elongator mutations confer resistance to the
RT Kluyveromyces lactis zymocin.";
RL EMBO J. 20:1993-2003(2001).
RN [6]
RP IDENTIFICATION IN THE ELONGATOR COMPLEX.
RX PubMed=11435442; DOI=10.1074/jbc.m105303200;
RA Winkler G.S., Petrakis T.G., Ethelberg S., Tokunaga M.,
RA Erdjument-Bromage H., Tempst P., Svejstrup J.Q.;
RT "RNA polymerase II elongator holoenzyme is composed of two discrete
RT subcomplexes.";
RL J. Biol. Chem. 276:32743-32749(2001).
RN [7]
RP IDENTIFICATION IN THE ELONGATOR COMPLEX, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RX PubMed=11390369; DOI=10.1074/jbc.c100274200;
RA Li Y., Takagi Y., Jiang Y., Tokunaga M., Erdjument-Bromage H., Tempst P.,
RA Kornberg R.D.;
RT "A multiprotein complex that interacts with RNA polymerase II elongator.";
RL J. Biol. Chem. 276:29628-29631(2001).
RN [8]
RP IDENTIFICATION IN THE ELONGATOR COMPLEX.
RX PubMed=11689709; DOI=10.1128/mcb.21.23.8203-8212.2001;
RA Krogan N.J., Greenblatt J.F.;
RT "Characterization of a six-subunit holo-elongator complex required for the
RT regulated expression of a group of genes in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 21:8203-8212(2001).
RN [9]
RP DISPUTED FUNCTION IN HISTONE ACETYLATION.
RX PubMed=11904415; DOI=10.1073/pnas.022042899;
RA Winkler G.S., Kristjuhan A., Erdjument-Bromage H., Tempst P.,
RA Svejstrup J.Q.;
RT "Elongator is a histone H3 and H4 acetyltransferase important for normal
RT histone acetylation levels in vivo.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:3517-3522(2002).
RN [10]
RP FUNCTION OF THE ELONGATOR COMPLEX IN PICHIA INOSITOVORA TOXIN SENSITIVITY.
RX PubMed=13680368; DOI=10.1007/s00438-003-0920-5;
RA Klassen R., Meinhardt F.;
RT "Structural and functional analysis of the killer element pPin1-3 from
RT Pichia inositovora.";
RL Mol. Genet. Genomics 270:190-199(2003).
RN [11]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [12]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [13]
RP SUBCELLULAR LOCATION.
RX PubMed=15780940; DOI=10.1016/j.molcel.2005.02.018;
RA Rahl P.B., Chen C.Z., Collins R.N.;
RT "Elp1p, the yeast homolog of the FD disease syndrome protein, negatively
RT regulates exocytosis independently of transcriptional elongation.";
RL Mol. Cell 17:841-853(2005).
RN [14]
RP FUNCTION IN TRNA MODIFICATION.
RX PubMed=15769872; DOI=10.1261/rna.7247705;
RA Huang B., Johansson M.J.O., Bystroem A.S.;
RT "An early step in wobble uridine tRNA modification requires the Elongator
RT complex.";
RL RNA 11:424-436(2005).
RN [15]
RP INTERACTION WITH KTI11.
RX PubMed=18627462; DOI=10.1111/j.1365-2958.2008.06350.x;
RA Baer C., Zabel R., Liu S., Stark M.J., Schaffrath R.;
RT "A versatile partner of eukaryotic protein complexes that is involved in
RT multiple biological processes: Kti11/Dph3.";
RL Mol. Microbiol. 69:1221-1233(2008).
RN [16]
RP PHOSPHORYLATION AT SER-3 AND SER-4.
RX PubMed=25569479; DOI=10.1371/journal.pgen.1004931;
RA Abdel-Fattah W., Jablonowski D., Di Santo R., Thuering K.L., Scheidt V.,
RA Hammermeister A., Ten Have S., Helm M., Schaffrath R., Stark M.J.;
RT "Phosphorylation of Elp1 by Hrr25 is required for elongator-dependent tRNA
RT modification in yeast.";
RL PLoS Genet. 11:e1004931-e1004931(2015).
RN [17]
RP REVIEW.
RX PubMed=29332244; DOI=10.1007/s00018-018-2747-6;
RA Dalwadi U., Yip C.K.;
RT "Structural insights into the function of Elongator.";
RL Cell. Mol. Life Sci. 75:1613-1622(2018).
RN [18]
RP SUBUNIT.
RX PubMed=31309145; DOI=10.1126/sciadv.aaw2326;
RA Dauden M.I., Jaciuk M., Weis F., Lin T.Y., Kleindienst C., Abbassi N.E.H.,
RA Khatter H., Krutyholowa R., Breunig K.D., Kosinski J., Mueller C.W.,
RA Glatt S.;
RT "Molecular basis of tRNA recognition by the Elongator complex.";
RL Sci. Adv. 5:eaaw2326-eaaw2326(2019).
RN [19] {ECO:0007744|PDB:4EJS}
RP X-RAY CRYSTALLOGRAPHY (2.61 ANGSTROMS) OF 1-238.
RX PubMed=22556426; DOI=10.1074/jbc.m112.341560;
RA Lin Z., Zhao W., Diao W., Xie X., Wang Z., Zhang J., Shen Y., Long J.;
RT "Crystal structure of elongator subcomplex Elp4-6.";
RL J. Biol. Chem. 287:21501-21508(2012).
RN [20] {ECO:0007744|PDB:4A8J}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 1-270, AND SUBUNIT.
RX PubMed=22343726; DOI=10.1038/nsmb.2234;
RA Glatt S., Letoquart J., Faux C., Taylor N.M., Seraphin B., Muller C.W.;
RT "The Elongator subcomplex Elp456 is a hexameric RecA-like ATPase.";
RL Nat. Struct. Mol. Biol. 19:314-320(2012).
RN [21]
RP STRUCTURE BY ELECTRON MICROSCOPY (3.3 ANGSTROMS), AND IDENTIFICATION IN THE
RP ELONGATOR COMPLEX.
RX PubMed=27974378; DOI=10.15252/embr.201643353;
RA Dauden M.I., Kosinski J., Kolaj-Robin O., Desfosses A., Ori A., Faux C.,
RA Hoffmann N.A., Onuma O.F., Breunig K.D., Beck M., Sachse C., Seraphin B.,
RA Glatt S., Mueller C.W.;
RT "Architecture of the yeast Elongator complex.";
RL EMBO Rep. 18:264-279(2017).
RN [22]
RP STRUCTURE BY ELECTRON MICROSCOPY, AND IDENTIFICATION IN THE ELONGATOR
RP COMPLEX.
RX PubMed=27872205; DOI=10.15252/embr.201642548;
RA Setiaputra D.T., Cheng D.T., Lu S., Hansen J.M., Dalwadi U., Lam C.H.,
RA To J.L., Dong M.Q., Yip C.K.;
RT "Molecular architecture of the yeast Elongator complex reveals an
RT unexpected asymmetric subunit arrangement.";
RL EMBO Rep. 18:280-291(2017).
CC -!- FUNCTION: Component of the elongator complex which is required for
CC multiple tRNA modifications, including mcm5U (5-methoxycarbonylmethyl
CC uridine), mcm5s2U (5-methoxycarbonylmethyl-2-thiouridine), and ncm5U
CC (5-carbamoylmethyl uridine) (PubMed:15769872). The elongator complex
CC catalyzes formation of carboxymethyluridine in the wobble base at
CC position 34 in tRNAs (PubMed:29332244). It functions as a gamma-toxin
CC target (TOT); disruption of the complex confers resistance to
CC Kluyveromyces lactis toxin zymocin (pGKL1 killer toxin)
CC (PubMed:11296232). May also be involved in sensitivity to Pichia
CC inositovora toxin. {ECO:0000269|PubMed:11296232,
CC ECO:0000269|PubMed:13680368, ECO:0000269|PubMed:15769872,
CC ECO:0000303|PubMed:29332244}.
CC -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC biosynthesis. {ECO:0000269|PubMed:15769872}.
CC -!- SUBUNIT: Component of the elongator complex, which consists of
CC ELP1/IKI3, ELP2, ELP3, ELP4, ELP5/IKI1 and ELP6 (PubMed:11435442,
CC PubMed:11390369, PubMed:11689709, PubMed:27974378, PubMed:27872205).
CC The elongator complex is composed of two copies of the Elp123
CC subcomplex (composed of ELP1/IKI3, ELP2 and ELP3) and two copies of the
CC Elp456 subcomplex (composed of ELP4, ELP5/IKI1 and ELP6)
CC (PubMed:27974378, PubMed:27872205). The Elp123 subcomplex forms a two-
CC lobed scaffold, which binds the Elp456 subcomplex asymmetrically
CC (PubMed:27974378, PubMed:27872205). In each lobe, ELP2 is tightly
CC sandwiched between ELP1/IKI3 and ELP3 (PubMed:31309145). The Elp123
CC subcomplex binds tRNA through ELP1/IKI3 and ELP3 and can bind 2 tRNAs
CC simultaneously (PubMed:31309145). tRNA-binding by the Elp123 subcomplex
CC induces conformational rearrangements which precisely position the
CC targeted anticodon base in the active site (PubMed:31309145). The
CC Elp456 subcomplex binds tRNA and has ATPase activity (PubMed:22556426,
CC PubMed:22343726). Interacts with KTI11/DPH3 (PubMed:18627462).
CC {ECO:0000269|PubMed:11390369, ECO:0000269|PubMed:11435442,
CC ECO:0000269|PubMed:11689709, ECO:0000269|PubMed:18627462,
CC ECO:0000269|PubMed:22343726, ECO:0000269|PubMed:22556426,
CC ECO:0000269|PubMed:27872205, ECO:0000269|PubMed:27974378,
CC ECO:0000269|PubMed:31309145}.
CC -!- INTERACTION:
CC P38874; P42935: ELP2; NbExp=5; IntAct=EBI-9061, EBI-23459;
CC P38874; Q02908: ELP3; NbExp=6; IntAct=EBI-9061, EBI-33957;
CC P38874; Q02884: ELP4; NbExp=13; IntAct=EBI-9061, EBI-35277;
CC P38874; Q04868: ELP6; NbExp=7; IntAct=EBI-9061, EBI-27653;
CC P38874; P38874: IKI1; NbExp=2; IntAct=EBI-9061, EBI-9061;
CC P38874; Q06706: IKI3; NbExp=10; IntAct=EBI-9061, EBI-9068;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15780940}. Nucleus
CC {ECO:0000269|PubMed:10024884}.
CC -!- MISCELLANEOUS: Present with 3870 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the ELP5 family. {ECO:0000305}.
CC -!- CAUTION: The elongator complex was originally thought to play a role in
CC transcription elongation. However, it is no longer thought to play a
CC direct role in this process and its primary function is thought to be
CC in tRNA modification. {ECO:0000305|PubMed:10024884,
CC ECO:0000305|PubMed:11689709, ECO:0000305|PubMed:11904415,
CC ECO:0000305|PubMed:29332244}.
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DR EMBL; D83267; BAA20087.1; -; Genomic_DNA.
DR EMBL; U00030; AAB68362.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06879.1; -; Genomic_DNA.
DR PIR; S46684; S46684.
DR RefSeq; NP_012057.3; NM_001179318.3.
DR PDB; 4A8J; X-ray; 2.10 A; B/E=1-270.
DR PDB; 4EJS; X-ray; 2.61 A; B=1-238.
DR PDBsum; 4A8J; -.
DR PDBsum; 4EJS; -.
DR AlphaFoldDB; P38874; -.
DR SMR; P38874; -.
DR BioGRID; 36621; 179.
DR ComplexPortal; CPX-779; Elongator holoenzyme complex.
DR DIP; DIP-1967N; -.
DR IntAct; P38874; 10.
DR MINT; P38874; -.
DR STRING; 4932.YHR187W; -.
DR MaxQB; P38874; -.
DR PaxDb; P38874; -.
DR PRIDE; P38874; -.
DR DNASU; 856594; -.
DR EnsemblFungi; YHR187W_mRNA; YHR187W; YHR187W.
DR GeneID; 856594; -.
DR KEGG; sce:YHR187W; -.
DR SGD; S000001230; IKI1.
DR VEuPathDB; FungiDB:YHR187W; -.
DR eggNOG; ENOG502QQIZ; Eukaryota.
DR GeneTree; ENSGT00390000009210; -.
DR HOGENOM; CLU_050414_1_0_1; -.
DR InParanoid; P38874; -.
DR OMA; ELLHFMA; -.
DR BioCyc; YEAST:G3O-31217-MON; -.
DR UniPathway; UPA00988; -.
DR PRO; PR:P38874; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38874; protein.
DR GO; GO:0005737; C:cytoplasm; IDA:SGD.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0033588; C:elongator holoenzyme complex; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0006417; P:regulation of translation; IC:ComplexPortal.
DR GO; GO:0006400; P:tRNA modification; IMP:SGD.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IC:ComplexPortal.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR019519; Elp5.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR15641; PTHR15641; 1.
DR Pfam; PF10483; Elong_Iki1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Nucleus; Phosphoprotein; Reference proteome;
KW tRNA processing.
FT CHAIN 1..309
FT /note="Elongator complex protein 5"
FT /id="PRO_0000084178"
FT MOD_RES 3
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:25569479"
FT MOD_RES 4
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:25569479"
FT HELIX 8..16
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 23..30
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 36..48
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 55..61
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 70..74
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 102..107
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 109..111
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 114..116
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 117..124
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 129..136
FT /evidence="ECO:0007829|PDB:4A8J"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:4EJS"
FT HELIX 157..164
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 166..173
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 181..189
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 200..209
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 215..223
FT /evidence="ECO:0007829|PDB:4A8J"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:4A8J"
SQ SEQUENCE 309 AA; 35220 MW; DFD93D7BA583E2F5 CRC64;
MASSSHNPVI LLKRILSLTE SSPFILCLDS IAQTSYKLIQ EFVHQSKSKG NEYPIVYISF
ETVNKPSYCT QFIDATQMDF VHLVKQIISY LPAATATQAK KHMVIIDSLN YISTEYITRF
LSEIASPHCT MVATYHKDIK DENRTVIPDW NNNYPDKLTL LQFMATTIVD IDVVLTGTLD
TEEVSELLNE FRIPRGLNND IFQLRLVNKR KSGRSLEYDF IVNSNTHEYE LLSTTKQEEE
SSSNGLETPE MLQGLTTFNL GTSNKQKLAK DQVALPFLEA QSFGQGGAIV YEYEKDDDYD
EEDPYEDPF
