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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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1508 – 155548RING-typePROSITE-ProRule annotationAdd
BLAST

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 modification 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)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi1542 – 15421W → A or E: Abolishes ability to control levels of proteins with 'non-stop'. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 15621562E3 ubiquitin-protein ligase listerinPRO_0000056341Add
BLAST

Proteomic databases

MaxQBiQ04781.

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 interactions.
IntActiQ04781. 3 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ04781.
SMRiQ04781. Positions 1503-1559.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati41 – 7838HEAT 1Sequence analysisAdd
BLAST
Repeati127 – 16438HEAT 2Sequence analysisAdd
BLAST
Repeati175 – 21743HEAT 3Sequence analysisAdd
BLAST
Repeati262 – 30140HEAT 4Sequence analysisAdd
BLAST
Repeati304 – 34845HEAT 5Sequence analysisAdd
BLAST
Repeati495 – 53238HEAT 6Sequence analysisAdd
BLAST
Repeati555 – 59238HEAT 7Sequence analysisAdd
BLAST
Repeati813 – 85038HEAT 8Sequence analysisAdd
BLAST
Repeati908 – 94538HEAT 9Sequence analysisAdd
BLAST
Repeati997 – 103741HEAT 10Sequence analysisAdd
BLAST
Repeati1047 – 108539HEAT 11Sequence analysisAdd
BLAST
Repeati1188 – 122639HEAT 12Sequence analysisAdd
BLAST
Repeati1263 – 129836HEAT 13Sequence analysisAdd
BLAST
Repeati1299 – 133941HEAT 14Sequence analysisAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri1508 – 155548RING-typePROSITE-ProRule annotationAdd
BLAST

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

ProteinModelPortaliQ04781.
SMRiQ04781. Positions 1503-1559.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi35426. 119 interactions.
IntActiQ04781. 3 interactions.

PTM databases

iPTMnetiQ04781.

Proteomic databases

MaxQBiQ04781.

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: September 7, 2016
This is version 127 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

Complete proteome, Reference proteome

Documents

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