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Protein

E3 ubiquitin-protein ligase listerin

Gene

RKR1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation (PubMed:23178123). Mediates ubiquitination of proteins derived from mRNAs lacking stop codons (non-stop proteins) and other translation arrest products induced by poly-lysine sequences and tandem rare codons. Ubiquitination leads to CDC48 recruitment for extraction and degradation of the incomplete translation product (PubMed:20835226, PubMed:23825054, PubMed:24261871). May indirectly play a role in chromatin function and transcription (PubMed:17283062).5 Publications

Pathwayi: protein ubiquitination

This protein is involved in the pathway protein ubiquitination, which is part of Protein modification.
View all proteins of this organism that are known to be involved in the pathway protein ubiquitination and in Protein modification.

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1508 – 1555RING-typePROSITE-ProRule annotationAdd BLAST48

GO - Molecular functioni

  • ligase activity Source: UniProtKB-KW
  • ribosomal large subunit binding Source: SGD
  • ubiquitin-protein transferase activity Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • chromatin organization Source: SGD
  • chromatin silencing at telomere Source: SGD
  • proteasomal protein catabolic process Source: SGD
  • protein ubiquitination Source: SGD
  • rescue of stalled ribosome Source: SGD
  • ribosome-associated ubiquitin-dependent protein catabolic process Source: SGD
  • ubiquitin-dependent protein catabolic process Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Ubl conjugation pathway

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-32926-MONOMER.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase listerin1 Publication (EC:6.3.2.-)
Alternative name(s):
RING domain mutant killed by rtf1 deletion protein 11 Publication
Gene namesi
Name:RKR11 Publication
Synonyms:LTN11 Publication
Ordered Locus Names:YMR247CImported
ORF Names:YM9408.09C, YM9920.01C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XIII

Organism-specific databases

EuPathDBiFungiDB:YMR247C.
SGDiS000004861. RKR1.

Subcellular locationi

GO - Cellular componenti

  • chromosome, telomeric region Source: GOC
  • nucleus Source: SGD
  • RQC complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi1542W → A or E: Abolishes ability to control levels of proteins with 'non-stop'. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000563411 – 1562E3 ubiquitin-protein ligase listerinAdd BLAST1562

Proteomic databases

MaxQBiQ04781.
PRIDEiQ04781.

PTM databases

iPTMnetiQ04781.

Interactioni

Subunit structurei

Component of the ribosome quality control complex (RQC), composed of the E3 ubiquitin ligase RKR1/LTN1, RQC1 and RQC2, as well as CDC48 and its ubiquitin-binding cofactors. RQC forms a stable complex with 60S ribosomal subunits (PubMed:23178123, PubMed:23479637, PubMed:25349383).3 Publications

Protein-protein interaction databases

BioGridi35426. 119 interactors.
IntActiQ04781. 3 interactors.

Structurei

Secondary structure

11562
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi21 – 23Combined sources3
Beta strandi27 – 32Combined sources6
Helixi36 – 40Combined sources5
Helixi45 – 54Combined sources10
Helixi59 – 74Combined sources16
Turni75 – 78Combined sources4
Helixi80 – 82Combined sources3
Helixi85 – 98Combined sources14
Helixi104 – 120Combined sources17
Turni122 – 125Combined sources4
Helixi126 – 128Combined sources3
Helixi129 – 140Combined sources12
Helixi145 – 158Combined sources14
Turni159 – 161Combined sources3
Helixi163 – 172Combined sources10
Helixi174 – 185Combined sources12
Helixi190 – 193Combined sources4
Turni196 – 198Combined sources3
Helixi201 – 225Combined sources25
Helixi229 – 232Combined sources4
Helixi234 – 242Combined sources9
Beta strandi243 – 246Combined sources4
Helixi247 – 249Combined sources3
Beta strandi253 – 256Combined sources4
Helixi259 – 273Combined sources15
Helixi276 – 279Combined sources4
Helixi281 – 294Combined sources14
Helixi295 – 297Combined sources3
Turni300 – 302Combined sources3
Helixi303 – 306Combined sources4
Helixi307 – 309Combined sources3
Helixi310 – 320Combined sources11
Turni321 – 326Combined sources6
Helixi327 – 331Combined sources5
Helixi335 – 346Combined sources12
Helixi354 – 365Combined sources12
Helixi366 – 368Combined sources3
Turni373 – 376Combined sources4
Helixi377 – 391Combined sources15
Helixi398 – 413Combined sources16
Turni414 – 419Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FG0X-ray2.41A/B13-424[»]
5FG1X-ray2.55A13-424[»]
ProteinModelPortaliQ04781.
SMRiQ04781.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Repeati41 – 78HEAT 1Sequence analysisAdd BLAST38
Repeati127 – 164HEAT 2Sequence analysisAdd BLAST38
Repeati175 – 217HEAT 3Sequence analysisAdd BLAST43
Repeati262 – 301HEAT 4Sequence analysisAdd BLAST40
Repeati304 – 348HEAT 5Sequence analysisAdd BLAST45
Repeati495 – 532HEAT 6Sequence analysisAdd BLAST38
Repeati555 – 592HEAT 7Sequence analysisAdd BLAST38
Repeati813 – 850HEAT 8Sequence analysisAdd BLAST38
Repeati908 – 945HEAT 9Sequence analysisAdd BLAST38
Repeati997 – 1037HEAT 10Sequence analysisAdd BLAST41
Repeati1047 – 1085HEAT 11Sequence analysisAdd BLAST39
Repeati1188 – 1226HEAT 12Sequence analysisAdd BLAST39
Repeati1263 – 1298HEAT 13Sequence analysisAdd BLAST36
Repeati1299 – 1339HEAT 14Sequence analysisAdd BLAST41

Sequence similaritiesi

Belongs to the LTN1 family.Curated
Contains 14 HEAT repeats.Sequence analysis
Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1508 – 1555RING-typePROSITE-ProRule annotationAdd BLAST48

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00390000016055.
InParanoidiQ04781.
OMAiDEQTMEM.
OrthoDBiEOG092C029X.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR016024. ARM-type_fold.
IPR001841. Znf_RING.
IPR011016. Znf_RING-CH.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00744. RINGv. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 3 hits.
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q04781-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSFGGINTFQ QYNTDLGLGH NGVRISLNYF DGLPDPSLLN SLYSNELKLI
60 70 80 90 100
FKSLLKRDET TKEKALMDLS NLISDFNQNE YFFNDIFLLC WSQIYAKLII
110 120 130 140 150
SDYKVIRLQS HQITIMLVKS LRKKISKFLK DFIPLILLGT CELDYSVSKP
160 170 180 190 200
SLNELTECFN KDPAKINALW AVFQEQLLNL VKEIVVNENE DTISDERYSS
210 220 230 240 250
KEESEFRYHR VIASAVLLLI KLFVHNKDVS ERNSSSLKVI LSDESIWKLL
260 270 280 290 300
NLKNGQNTNA YETVLRLIDV LYTRGYMPSH KNIMKLAVKK LLKSLTHITS
310 320 330 340 350
KNILKVCPVL PSILNLLATL DDYEDGTIWS YDKSSKEKVL KFLSVSRTSP
360 370 380 390 400
SPGFFNAVFA LYSSTKRHSF LDYYLEWLPF WQKSVQRLNE KGFSARNSAE
410 420 430 440 450
VLNEFWTNFL KFAEDSSEER VKKMVESEIF NSLSCGKSLS EYTKLNQTLS
460 470 480 490 500
GVFPPDKWER EIEDYFTSDE DIRKIKVSFE KNLFALLVTS PNNESAISRL
510 520 530 540 550
FDFFVQLIET DPSNVFNKYD GVYDALNYFL DSDMIFLNGK IGKFINEIPT
560 570 580 590 600
LVQESTYQNF AGIMAQYSNS KFFKMNTDAI TSLEDFFIVA LSFNLPKTII
610 620 630 640 650
LATMNELDND IYQQLMKSDS LELELYIEDF MKNYKFDDSG EIFKGNNKFL
660 670 680 690 700
NQRTITTLYR SAVANGQVEQ FCAVLSKLDE TFFSTLLLNT DFLSCALYEV
710 720 730 740 750
SEDTNEKLFK LSLQLAKGNS EIANKLAQVI LQHAQVYFSP GAKEKYVTHA
760 770 780 790 800
VELINGCNDT SQIFFPANAI EVFARYMPAI DYRSSLVSSL STNTHLLLTD
810 820 830 840 850
DKPINLKNMQ KLIRYALFLD ALLDALPERV NNHIVAFITV VSELVTDYNC
860 870 880 890 900
LSEEPNDLYY DFGHTFFKHG KVNLNFSDIV GNVIQPANGG DAMLTFDIAE
910 920 930 940 950
SNSVYFFYYS RVLYKVLLNS IDTVSSTTLN GLLASVESFV TKTVRDQKST
960 970 980 990 1000
DKDYLLCAIL LLMFNRSNSK DEITKLRTLL ASQLIGIREV ELVDQEFKSL
1010 1020 1030 1040 1050
ALLNNLLDIP QADKQFVPIA PQRLNMIFRS ILKWLDSDLA YEPSFSTVRL
1060 1070 1080 1090 1100
LLLDFFTKLM RFEGVRDMGI TAFELSERLL ADSLSMCQID DTLYLLELRS
1110 1120 1130 1140 1150
SCLNLYETLS QGVSKNGEEI SEYGDEIQEN LIELMFLNFN QERNNQVSTL
1160 1170 1180 1190 1200
FYQKLYKVIS SMELKKLESQ YKRIFEVVLN DKDIGSNINQ SRLLTTLLGS
1210 1220 1230 1240 1250
LVVKTQQDII IEYELRIQKQ TGSDVDGSAS DNDVNSKFKL PQKLLQKVTD
1260 1270 1280 1290 1300
EVPKEYLEYE NKNSFIKYLW YWHLILMYFK DTSYNMRQIF IEQLKEAGLI
1310 1320 1330 1340 1350
NRMFDFITDQ IDLRDTEFWK QVDTKEISEY NIVGNNFSPY KEDIFEECKK
1360 1370 1380 1390 1400
LLGHTLYQLF NNVGCLTSIW WLNIKDRTLQ NDIEKFVSEF ISPILIKNEF
1410 1420 1430 1440 1450
DDINSKMDRL TSNDDALTIK LNNITNEVKA SYLIDDQKLE ISFKLPKNYP
1460 1470 1480 1490 1500
LTNIQVNGVS RVGISEQKWK QWIMSTQHVI TGMNGSVLDS LELFTKNVHL
1510 1520 1530 1540 1550
QFSGFEECAI CYSILHAVDR KLPSKTCPTC KNKFHGACLY KWFRSSGNNT
1560
CPLCRSEIPF RR
Length:1,562
Mass (Da):180,186
Last modified:November 1, 1997 - v1
Checksum:i97AC65E881362305
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48639 Genomic DNA. Translation: CAA88574.1.
Z48756 Genomic DNA. Translation: CAA88657.1.
BK006946 Genomic DNA. Translation: DAA10148.1.
PIRiS53069.
RefSeqiNP_013975.1. NM_001182755.1.

Genome annotation databases

EnsemblFungiiYMR247C; YMR247C; YMR247C.
GeneIDi855289.
KEGGisce:YMR247C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z48639 Genomic DNA. Translation: CAA88574.1.
Z48756 Genomic DNA. Translation: CAA88657.1.
BK006946 Genomic DNA. Translation: DAA10148.1.
PIRiS53069.
RefSeqiNP_013975.1. NM_001182755.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5FG0X-ray2.41A/B13-424[»]
5FG1X-ray2.55A13-424[»]
ProteinModelPortaliQ04781.
SMRiQ04781.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35426. 119 interactors.
IntActiQ04781. 3 interactors.

PTM databases

iPTMnetiQ04781.

Proteomic databases

MaxQBiQ04781.
PRIDEiQ04781.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYMR247C; YMR247C; YMR247C.
GeneIDi855289.
KEGGisce:YMR247C.

Organism-specific databases

EuPathDBiFungiDB:YMR247C.
SGDiS000004861. RKR1.

Phylogenomic databases

GeneTreeiENSGT00390000016055.
InParanoidiQ04781.
OMAiDEQTMEM.
OrthoDBiEOG092C029X.

Enzyme and pathway databases

UniPathwayiUPA00143.
BioCyciYEAST:G3O-32926-MONOMER.

Miscellaneous databases

PROiQ04781.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR016024. ARM-type_fold.
IPR001841. Znf_RING.
IPR011016. Znf_RING-CH.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00744. RINGv. 1 hit.
[Graphical view]
SUPFAMiSSF48371. SSF48371. 3 hits.
PROSITEiPS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiLTN1_YEAST
AccessioniPrimary (citable) accession number: Q04781
Secondary accession number(s): D6W074, Q04029
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1997
Last modified: November 2, 2016
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 222 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  5. Yeast chromosome XIII
    Yeast (Saccharomyces cerevisiae) chromosome XIII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.