ELP6_YEAST
ID ELP6_YEAST Reviewed; 273 AA.
AC Q04868; D6W0D9;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Elongator complex protein 6;
DE AltName: Full=Gamma-toxin target 6;
DE AltName: Full=HAT-associated protein 3;
GN Name=ELP6; Synonyms=HAP3, TOT6; OrderedLocusNames=YMR312W;
GN ORFNames=YM9924.04;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169872;
RA Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL Nature 387:90-93(1997).
RN [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
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.
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 [12]
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 [13]
RP FUNCTION.
RX PubMed=18755837; DOI=10.1261/rna.1184108;
RA Huang B., Lu J., Bystroem A.S.;
RT "A genome-wide screen identifies genes required for formation of the wobble
RT nucleoside 5-methoxycarbonylmethyl-2-thiouridine in Saccharomyces
RT cerevisiae.";
RL RNA 14:2183-2194(2008).
RN [14]
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 [15]
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 [16] {ECO:0007744|PDB:4EJS}
RP X-RAY CRYSTALLOGRAPHY (2.61 ANGSTROMS).
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 [17] {ECO:0007744|PDB:4A8J}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), 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 [18]
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 [19]
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, PubMed:18755837). The
CC elongator complex catalyzes formation of carboxymethyluridine in the
CC wobble base at position 34 in tRNAs (PubMed:29332244). It functions as
CC a gamma-toxin target (TOT); disruption of the complex confers
CC resistance to Kluyveromyces lactis toxin zymocin (pGKL1 killer toxin)
CC (PubMed:11296232). May also be involved in sensitivity to Pichia
CC inositovora toxin (PubMed:13680368). {ECO:0000269|PubMed:11296232,
CC ECO:0000269|PubMed:13680368, ECO:0000269|PubMed:15769872,
CC ECO:0000269|PubMed:18755837, ECO:0000303|PubMed:29332244}.
CC -!- PATHWAY: tRNA modification; 5-methoxycarbonylmethyl-2-thiouridine-tRNA
CC biosynthesis. {ECO:0000269|PubMed:15769872,
CC ECO:0000269|PubMed:18755837}.
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). {ECO:0000269|PubMed:11390369,
CC ECO:0000269|PubMed:11435442, ECO:0000269|PubMed:11689709,
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 Q04868; P42935: ELP2; NbExp=2; IntAct=EBI-27653, EBI-23459;
CC Q04868; Q02908: ELP3; NbExp=4; IntAct=EBI-27653, EBI-33957;
CC Q04868; Q02884: ELP4; NbExp=14; IntAct=EBI-27653, EBI-35277;
CC Q04868; Q04868: ELP6; NbExp=2; IntAct=EBI-27653, EBI-27653;
CC Q04868; P38874: IKI1; NbExp=7; IntAct=EBI-27653, EBI-9061;
CC Q04868; Q06706: IKI3; NbExp=7; IntAct=EBI-27653, EBI-9068;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15780940}. Nucleus
CC {ECO:0000269|PubMed:10024884}.
CC -!- SIMILARITY: Belongs to the ELP6 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; Z54141; CAA90830.1; -; Genomic_DNA.
DR EMBL; AY557983; AAS56309.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10213.1; -; Genomic_DNA.
DR PIR; S59305; S59305.
DR RefSeq; NP_014043.1; NM_001182823.1.
DR PDB; 4A8J; X-ray; 2.10 A; C/F=1-273.
DR PDB; 4EJS; X-ray; 2.61 A; C=1-273.
DR PDBsum; 4A8J; -.
DR PDBsum; 4EJS; -.
DR AlphaFoldDB; Q04868; -.
DR SMR; Q04868; -.
DR BioGRID; 35492; 462.
DR ComplexPortal; CPX-779; Elongator holoenzyme complex.
DR DIP; DIP-1966N; -.
DR IntAct; Q04868; 9.
DR MINT; Q04868; -.
DR STRING; 4932.YMR312W; -.
DR CarbonylDB; Q04868; -.
DR MaxQB; Q04868; -.
DR PaxDb; Q04868; -.
DR PRIDE; Q04868; -.
DR DNASU; 855360; -.
DR EnsemblFungi; YMR312W_mRNA; YMR312W; YMR312W.
DR GeneID; 855360; -.
DR KEGG; sce:YMR312W; -.
DR SGD; S000004929; ELP6.
DR VEuPathDB; FungiDB:YMR312W; -.
DR eggNOG; ENOG502QSI3; Eukaryota.
DR HOGENOM; CLU_086730_0_0_1; -.
DR InParanoid; Q04868; -.
DR OMA; EYVYHIT; -.
DR BioCyc; YEAST:G3O-32976-MON; -.
DR UniPathway; UPA00988; -.
DR PRO; PR:Q04868; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q04868; protein.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0033588; C:elongator holoenzyme complex; IDA:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0032447; P:protein urmylation; IMP:SGD.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0006417; P:regulation of translation; IC:ComplexPortal.
DR GO; GO:0002098; P:tRNA wobble uridine modification; IMP:SGD.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR018627; ELP6.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR16184; PTHR16184; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Nucleus; Reference proteome; tRNA processing.
FT CHAIN 1..273
FT /note="Elongator complex protein 6"
FT /id="PRO_0000203355"
FT HELIX 20..23
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 25..27
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 30..36
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 43..55
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 76..84
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 86..95
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 100..102
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 103..109
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 112..116
FT /evidence="ECO:0007829|PDB:4A8J"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 122..138
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 143..149
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 154..157
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 163..169
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 171..176
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 179..186
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 188..190
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 197..200
FT /evidence="ECO:0007829|PDB:4A8J"
FT HELIX 202..214
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 216..222
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 234..240
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 257..264
FT /evidence="ECO:0007829|PDB:4A8J"
FT STRAND 267..271
FT /evidence="ECO:0007829|PDB:4A8J"
SQ SEQUENCE 273 AA; 30574 MW; 1A5062465AF67F47 CRC64;
MGSVQRQDLV LFSDQSVLPA HFFQDSNSHN LFFITHQSCT QPLWMINALV ETHVLGSPSS
LNESSSSMLP SSTRSHAVLA SFIHEQNYFT NSLNKLKIPS NNYNVLDFLS DFIVNNIHNK
PRDKILSDVL AKFSAAIQNN PTDTIVIIEQ PELLLSLVSG LTCSELNNKF ITPLLRQCKV
LIIVSNSDIF NIDEYDASVH SSNLQNFYKS SFIKSMINLN LNPLKTGFAK DVTGSLHVCR
GGAPIATSNT SLHVVENEYL YLNEKESTKL FYR
