LTN1_YEAST
ID LTN1_YEAST Reviewed; 1562 AA.
AC Q04781; D6W074; Q04029;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 1.
DT 03-AUG-2022, entry version 167.
DE RecName: Full=E3 ubiquitin-protein ligase listerin {ECO:0000303|PubMed:20835226};
DE EC=2.3.2.27 {ECO:0000269|PubMed:17283062};
DE AltName: Full=RING domain mutant killed by rtf1 deletion protein 1 {ECO:0000303|PubMed:17283062};
DE AltName: Full=RING-type E3 ubiquitin transferase listerin {ECO:0000305};
GN Name=RKR1 {ECO:0000303|PubMed:17283062};
GN Synonyms=LTN1 {ECO:0000303|PubMed:20835226};
GN OrderedLocusNames=YMR247C {ECO:0000312|SGD:S000004861};
GN ORFNames=YM9408.09C, YM9920.01C;
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 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 [4]
RP FUNCTION, CATALYTIC ACTIVITY, PATHWAY, SUBCELLULAR LOCATION, AND
RP MUTAGENESIS OF CYS-1508.
RX PubMed=17283062; DOI=10.1128/mcb.01947-06;
RA Braun M.A., Costa P.J., Crisucci E.M., Arndt K.M.;
RT "Identification of Rkr1, a nuclear RING domain protein with functional
RT connections to chromatin modification in Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 27:2800-2811(2007).
RN [5]
RP FUNCTION, RIBOSOME-BINDING, SUBCELLULAR LOCATION, AND MUTAGENESIS OF
RP TRP-1542.
RX PubMed=20835226; DOI=10.1038/nature09371;
RA Bengtson M.H., Joazeiro C.A.;
RT "Role of a ribosome-associated E3 ubiquitin ligase in protein quality
RT control.";
RL Nature 467:470-473(2010).
RN [6]
RP FUNCTION, AND SUBUNIT.
RX PubMed=23178123; DOI=10.1016/j.cell.2012.10.044;
RA Brandman O., Stewart-Ornstein J., Wong D., Larson A., Williams C.C.,
RA Li G.W., Zhou S., King D., Shen P.S., Weibezahn J., Dunn J.G., Rouskin S.,
RA Inada T., Frost A., Weissman J.S.;
RT "A ribosome-bound quality control complex triggers degradation of nascent
RT peptides and signals translation stress.";
RL Cell 151:1042-1054(2012).
RN [7]
RP SUBUNIT.
RX PubMed=23479637; DOI=10.1073/pnas.1221724110;
RA Defenouillere Q., Yao Y., Mouaikel J., Namane A., Galopier A., Decourty L.,
RA Doyen A., Malabat C., Saveanu C., Jacquier A., Fromont-Racine M.;
RT "Cdc48-associated complex bound to 60S particles is required for the
RT clearance of aberrant translation products.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:5046-5051(2013).
RN [8]
RP FUNCTION.
RX PubMed=23825054; DOI=10.1261/rna.039446.113;
RA Letzring D.P., Wolf A.S., Brule C.E., Grayhack E.J.;
RT "Translation of CGA codon repeats in yeast involves quality control
RT components and ribosomal protein L1.";
RL RNA 19:1208-1217(2013).
RN [9]
RP FUNCTION.
RX PubMed=24261871; DOI=10.1111/gtc.12106;
RA Matsuda R., Ikeuchi K., Nomura S., Inada T.;
RT "Protein quality control systems associated with no-go and nonstop mRNA
RT surveillance in yeast.";
RL Genes Cells 19:1-12(2014).
RN [10]
RP SUBUNIT.
RX PubMed=25349383; DOI=10.1073/pnas.1413882111;
RA Lyumkis D., Oliveira dos Passos D., Tahara E.B., Webb K., Bennett E.J.,
RA Vinterbo S., Potter C.S., Carragher B., Joazeiro C.A.;
RT "Structural basis for translational surveillance by the large ribosomal
RT subunit-associated protein quality control complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 111:15981-15986(2014).
RN [11]
RP SUBUNIT.
RX PubMed=25554787; DOI=10.1126/science.1259724;
RA Shen P.S., Park J., Qin Y., Li X., Parsawar K., Larson M.H., Cox J.,
RA Cheng Y., Lambowitz A.M., Weissman J.S., Brandman O., Frost A.;
RT "Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-
RT independent elongation of nascent chains.";
RL Science 347:75-78(2015).
CC -!- FUNCTION: E3 ubiquitin-protein ligase component of the ribosome quality
CC control complex (RQC), a ribosome-associated complex that mediates
CC ubiquitination and extraction of incompletely synthesized nascent
CC chains for proteasomal degradation (PubMed:23178123). Mediates
CC ubiquitination of proteins derived from mRNAs lacking stop codons (non-
CC stop proteins) and other translation arrest products induced by poly-
CC lysine sequences and tandem rare codons. Ubiquitination leads to CDC48
CC recruitment for extraction and degradation of the incomplete
CC translation product (PubMed:20835226, PubMed:23825054,
CC PubMed:24261871). May indirectly play a role in chromatin function and
CC transcription (PubMed:17283062). {ECO:0000269|PubMed:17283062,
CC ECO:0000269|PubMed:20835226, ECO:0000269|PubMed:23178123,
CC ECO:0000269|PubMed:23825054, ECO:0000269|PubMed:24261871}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine +
CC [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-
CC cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.;
CC EC=2.3.2.27; Evidence={ECO:0000269|PubMed:17283062};
CC -!- PATHWAY: Protein modification; protein ubiquitination.
CC {ECO:0000269|PubMed:17283062}.
CC -!- SUBUNIT: Component of the ribosome quality control complex (RQC),
CC composed of the E3 ubiquitin ligase RKR1/LTN1, RQC1 and RQC2, as well
CC as CDC48 and its ubiquitin-binding cofactors associated with the 60S
CC ribosomal subunits (PubMed:23178123, PubMed:23479637, PubMed:25349383).
CC {ECO:0000269|PubMed:23178123, ECO:0000269|PubMed:23479637,
CC ECO:0000269|PubMed:25349383}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:17283062}. Cytoplasm,
CC cytosol {ECO:0000269|PubMed:20835226}.
CC -!- MISCELLANEOUS: Present with 222 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the LTN1 family. {ECO:0000305}.
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DR EMBL; Z48639; CAA88574.1; -; Genomic_DNA.
DR EMBL; Z48756; CAA88657.1; -; Genomic_DNA.
DR EMBL; BK006946; DAA10148.1; -; Genomic_DNA.
DR PIR; S53069; S53069.
DR RefSeq; NP_013975.1; NM_001182755.1.
DR PDB; 5FG0; X-ray; 2.41 A; A/B=13-424.
DR PDB; 5FG1; X-ray; 2.55 A; A=13-424.
DR PDBsum; 5FG0; -.
DR PDBsum; 5FG1; -.
DR AlphaFoldDB; Q04781; -.
DR SMR; Q04781; -.
DR BioGRID; 35426; 182.
DR ComplexPortal; CPX-3265; Ribosome quality control complex.
DR IntAct; Q04781; 3.
DR MINT; Q04781; -.
DR STRING; 4932.YMR247C; -.
DR iPTMnet; Q04781; -.
DR MaxQB; Q04781; -.
DR PaxDb; Q04781; -.
DR PRIDE; Q04781; -.
DR EnsemblFungi; YMR247C_mRNA; YMR247C; YMR247C.
DR GeneID; 855289; -.
DR KEGG; sce:YMR247C; -.
DR SGD; S000004861; RKR1.
DR VEuPathDB; FungiDB:YMR247C; -.
DR eggNOG; KOG0803; Eukaryota.
DR GeneTree; ENSGT00390000016055; -.
DR HOGENOM; CLU_262564_0_0_1; -.
DR InParanoid; Q04781; -.
DR OMA; NRFHGAC; -.
DR BioCyc; YEAST:G3O-32926-MON; -.
DR Reactome; R-SCE-983168; Antigen processing: Ubiquitination & Proteasome degradation.
DR UniPathway; UPA00143; -.
DR PRO; PR:Q04781; -.
DR Proteomes; UP000002311; Chromosome XIII.
DR RNAct; Q04781; protein.
DR GO; GO:0000781; C:chromosome, telomeric region; IEA:GOC.
DR GO; GO:0005829; C:cytosol; IDA:UniProtKB.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:1990112; C:RQC complex; IDA:SGD.
DR GO; GO:0043023; F:ribosomal large subunit binding; IDA:SGD.
DR GO; GO:0061630; F:ubiquitin protein ligase activity; IBA:GO_Central.
DR GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:SGD.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006325; P:chromatin organization; IGI:SGD.
DR GO; GO:0010498; P:proteasomal protein catabolic process; IMP:SGD.
DR GO; GO:0030163; P:protein catabolic process; IMP:SGD.
DR GO; GO:0016567; P:protein ubiquitination; IDA:SGD.
DR GO; GO:0072344; P:rescue of stalled ribosome; IMP:SGD.
DR GO; GO:1990116; P:ribosome-associated ubiquitin-dependent protein catabolic process; IMP:SGD.
DR GO; GO:0031509; P:subtelomeric heterochromatin assembly; IMP:SGD.
DR GO; GO:0006511; P:ubiquitin-dependent protein catabolic process; IMP:SGD.
DR CDD; cd16491; RING-CH-C4HC3_LTN1; 1.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR016024; ARM-type_fold.
DR InterPro; IPR039795; LTN1/Rkr1.
DR InterPro; IPR039804; RING-CH-C4HC3_LTN1.
DR InterPro; IPR001841; Znf_RING.
DR InterPro; IPR011016; Znf_RING-CH.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR PANTHER; PTHR12389; PTHR12389; 1.
DR Pfam; PF13639; zf-RING_2; 1.
DR SMART; SM00744; RINGv; 1.
DR SUPFAM; SSF48371; SSF48371; 1.
DR PROSITE; PS50089; ZF_RING_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Metal-binding; Nucleus; Reference proteome;
KW Repeat; Transferase; Ubl conjugation pathway; Zinc; Zinc-finger.
FT CHAIN 1..1562
FT /note="E3 ubiquitin-protein ligase listerin"
FT /id="PRO_0000056341"
FT REPEAT 41..78
FT /note="HEAT 1"
FT /evidence="ECO:0000255"
FT REPEAT 127..164
FT /note="HEAT 2"
FT /evidence="ECO:0000255"
FT REPEAT 175..217
FT /note="HEAT 3"
FT /evidence="ECO:0000255"
FT REPEAT 262..301
FT /note="HEAT 4"
FT /evidence="ECO:0000255"
FT REPEAT 304..348
FT /note="HEAT 5"
FT /evidence="ECO:0000255"
FT REPEAT 495..532
FT /note="HEAT 6"
FT /evidence="ECO:0000255"
FT REPEAT 555..592
FT /note="HEAT 7"
FT /evidence="ECO:0000255"
FT REPEAT 813..850
FT /note="HEAT 8"
FT /evidence="ECO:0000255"
FT REPEAT 908..945
FT /note="HEAT 9"
FT /evidence="ECO:0000255"
FT REPEAT 997..1037
FT /note="HEAT 10"
FT /evidence="ECO:0000255"
FT REPEAT 1047..1085
FT /note="HEAT 11"
FT /evidence="ECO:0000255"
FT REPEAT 1188..1226
FT /note="HEAT 12"
FT /evidence="ECO:0000255"
FT REPEAT 1263..1298
FT /note="HEAT 13"
FT /evidence="ECO:0000255"
FT REPEAT 1299..1339
FT /note="HEAT 14"
FT /evidence="ECO:0000255"
FT ZN_FING 1508..1555
FT /note="RING-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00175"
FT MUTAGEN 1508
FT /note="C->A: Abolishes catalytic activity."
FT /evidence="ECO:0000269|PubMed:17283062"
FT MUTAGEN 1542
FT /note="W->A,E: Abolishes ability to control levels of
FT proteins with 'non-stop'."
FT /evidence="ECO:0000269|PubMed:20835226"
FT STRAND 21..23
FT /evidence="ECO:0007829|PDB:5FG0"
FT STRAND 27..32
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 36..40
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 45..54
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 59..74
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 75..78
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 80..82
FT /evidence="ECO:0007829|PDB:5FG1"
FT HELIX 85..98
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 104..120
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 122..125
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 126..128
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 129..140
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 145..158
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 163..172
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 174..185
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 190..193
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 201..225
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 229..232
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 234..242
FT /evidence="ECO:0007829|PDB:5FG0"
FT STRAND 243..246
FT /evidence="ECO:0007829|PDB:5FG1"
FT HELIX 247..249
FT /evidence="ECO:0007829|PDB:5FG0"
FT STRAND 253..256
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 259..273
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 276..279
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 281..294
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 295..297
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 300..302
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 303..306
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 310..320
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 321..326
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 327..331
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 335..346
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 354..365
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 366..368
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 373..376
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 377..391
FT /evidence="ECO:0007829|PDB:5FG0"
FT HELIX 398..413
FT /evidence="ECO:0007829|PDB:5FG0"
FT TURN 414..419
FT /evidence="ECO:0007829|PDB:5FG0"
SQ SEQUENCE 1562 AA; 180186 MW; 97AC65E881362305 CRC64;
MSFGGINTFQ QYNTDLGLGH NGVRISLNYF DGLPDPSLLN SLYSNELKLI FKSLLKRDET
TKEKALMDLS NLISDFNQNE YFFNDIFLLC WSQIYAKLII SDYKVIRLQS HQITIMLVKS
LRKKISKFLK DFIPLILLGT CELDYSVSKP SLNELTECFN KDPAKINALW AVFQEQLLNL
VKEIVVNENE DTISDERYSS KEESEFRYHR VIASAVLLLI KLFVHNKDVS ERNSSSLKVI
LSDESIWKLL NLKNGQNTNA YETVLRLIDV LYTRGYMPSH KNIMKLAVKK LLKSLTHITS
KNILKVCPVL PSILNLLATL DDYEDGTIWS YDKSSKEKVL KFLSVSRTSP SPGFFNAVFA
LYSSTKRHSF LDYYLEWLPF WQKSVQRLNE KGFSARNSAE VLNEFWTNFL KFAEDSSEER
VKKMVESEIF NSLSCGKSLS EYTKLNQTLS GVFPPDKWER EIEDYFTSDE DIRKIKVSFE
KNLFALLVTS PNNESAISRL FDFFVQLIET DPSNVFNKYD GVYDALNYFL DSDMIFLNGK
IGKFINEIPT LVQESTYQNF AGIMAQYSNS KFFKMNTDAI TSLEDFFIVA LSFNLPKTII
LATMNELDND IYQQLMKSDS LELELYIEDF MKNYKFDDSG EIFKGNNKFL NQRTITTLYR
SAVANGQVEQ FCAVLSKLDE TFFSTLLLNT DFLSCALYEV SEDTNEKLFK LSLQLAKGNS
EIANKLAQVI LQHAQVYFSP GAKEKYVTHA VELINGCNDT SQIFFPANAI EVFARYMPAI
DYRSSLVSSL STNTHLLLTD DKPINLKNMQ KLIRYALFLD ALLDALPERV NNHIVAFITV
VSELVTDYNC LSEEPNDLYY DFGHTFFKHG KVNLNFSDIV GNVIQPANGG DAMLTFDIAE
SNSVYFFYYS RVLYKVLLNS IDTVSSTTLN GLLASVESFV TKTVRDQKST DKDYLLCAIL
LLMFNRSNSK DEITKLRTLL ASQLIGIREV ELVDQEFKSL ALLNNLLDIP QADKQFVPIA
PQRLNMIFRS ILKWLDSDLA YEPSFSTVRL LLLDFFTKLM RFEGVRDMGI TAFELSERLL
ADSLSMCQID DTLYLLELRS SCLNLYETLS QGVSKNGEEI SEYGDEIQEN LIELMFLNFN
QERNNQVSTL FYQKLYKVIS SMELKKLESQ YKRIFEVVLN DKDIGSNINQ SRLLTTLLGS
LVVKTQQDII IEYELRIQKQ TGSDVDGSAS DNDVNSKFKL PQKLLQKVTD EVPKEYLEYE
NKNSFIKYLW YWHLILMYFK DTSYNMRQIF IEQLKEAGLI NRMFDFITDQ IDLRDTEFWK
QVDTKEISEY NIVGNNFSPY KEDIFEECKK LLGHTLYQLF NNVGCLTSIW WLNIKDRTLQ
NDIEKFVSEF ISPILIKNEF DDINSKMDRL TSNDDALTIK LNNITNEVKA SYLIDDQKLE
ISFKLPKNYP LTNIQVNGVS RVGISEQKWK QWIMSTQHVI TGMNGSVLDS LELFTKNVHL
QFSGFEECAI CYSILHAVDR KLPSKTCPTC KNKFHGACLY KWFRSSGNNT CPLCRSEIPF
RR
