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Protein

E3 ubiquitin-protein ligase RLIM

Gene

Rlim

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase that acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone deacetylase corepressor complex. Ubiquitination and degradation of LIM cofactors LDB1 and LDB2 allows DNA-bound LIM homeodomain transcription factors to interact with other protein partners such as RLIM. Plays a role in telomere length-mediated growth suppression by mediating the ubiquitination and degradation of TERF1. By targeting ZFP42 for degradation, acts as an activator of random inactivation of X chromosome in the embryo, a stochastic process in which one X chromosome is inactivated to minimize sex-related dosage differences of X-encoded genes in somatic cells of female placental mammals.4 Publications

Catalytic activityi

S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6-ubiquitinyl-[acceptor protein]-L-lysine.

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 fingeri546 – 587RING-typePROSITE-ProRule annotationAdd BLAST42

GO - Molecular functioni

  • metal ion binding Source: UniProtKB-KW
  • ubiquitin protein ligase activity Source: MGI
  • ubiquitin-protein transferase activity Source: UniProtKB

GO - Biological processi

  • negative regulation of DNA binding transcription factor activity Source: MGI
  • negative regulation of transcription by RNA polymerase II Source: MGI
  • proteasome-mediated ubiquitin-dependent protein catabolic process Source: GO_Central
  • protein ubiquitination Source: UniProtKB
  • random inactivation of X chromosome Source: UniProtKB
  • regulation of dosage compensation by inactivation of X chromosome Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • ubiquitin-dependent protein catabolic process Source: UniProtKB

Keywordsi

Molecular functionTransferase
Biological processTranscription, Transcription regulation, Ubl conjugation pathway
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-983168 Antigen processing: Ubiquitination & Proteasome degradation
UniPathwayiUPA00143

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase RLIM (EC:2.3.2.27)
Alternative name(s):
LIM domain-interacting RING finger protein
RING finger LIM domain-binding protein
Short name:
R-LIM
RING finger protein 12
RING-type E3 ubiquitin transferase RLIMCurated
Gene namesi
Name:Rlim
Synonyms:Rnf12
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome X

Organism-specific databases

MGIiMGI:1342291 Rlim

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000560531 – 600E3 ubiquitin-protein ligase RLIMAdd BLAST600

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineBy similarity1
Modified residuei163PhosphoserineCombined sources1
Modified residuei194PhosphoserineBy similarity1
Modified residuei227PhosphoserineCombined sources1
Modified residuei229PhosphoserineCombined sources1
Modified residuei269PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ9WTV7
MaxQBiQ9WTV7
PaxDbiQ9WTV7
PeptideAtlasiQ9WTV7
PRIDEiQ9WTV7

PTM databases

iPTMnetiQ9WTV7
PhosphoSitePlusiQ9WTV7

Expressioni

Developmental stagei

Ubiquitously expressed in early development. Expressed in the time window of embryonic stem (ES) cell differentiation.1 Publication

Inductioni

Expressed at higher level in female compared to males cells (at protein level).1 Publication

Gene expression databases

BgeeiENSMUSG00000056537
CleanExiMM_RNF12
GenevisibleiQ9WTV7 MM

Interactioni

Subunit structurei

Interacts (via N-terminus) with TERF1. Interacts (via C-terminus) with ESR1 (By similarity). Interacts with LIM/homeobox factors such as LHX3. Interacts with LDB1, LDB2 and SIN3A. Interacts with LIMK1.By similarity2 Publications

Binary interactionsi

Show more details

Protein-protein interaction databases

BioGridi202918, 4 interactors
DIPiDIP-46445N
IntActiQ9WTV7, 10 interactors
STRINGi10090.ENSMUSP00000070662

Structurei

3D structure databases

ProteinModelPortaliQ9WTV7
SMRiQ9WTV7
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi597 – 600PDZ-bindingSequence analysis4

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi415 – 484Ser-richAdd BLAST70
Compositional biasi447 – 461Poly-SerAdd BLAST15

Sequence similaritiesi

Belongs to the RNF12 family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri546 – 587RING-typePROSITE-ProRule annotationAdd BLAST42

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0800 Eukaryota
ENOG41121N2 LUCA
GeneTreeiENSGT00730000110459
HOGENOMiHOG000273881
InParanoidiQ9WTV7
KOiK16271
OMAiMRNFGES
OrthoDBiEOG091G0B6K
PhylomeDBiQ9WTV7
TreeFamiTF325756

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR001841 Znf_RING
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF13639 zf-RING_2, 1 hit
SMARTiView protein in SMART
SM00184 RING, 1 hit
PROSITEiView protein in PROSITE
PS50089 ZF_RING_2, 1 hit

Sequencei

Sequence statusi: Complete.

Q9WTV7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MENSDSNDKG SDQSAAQRRS QMDRLDREEA FYQFVNNLSE EDYRLMRDNN
60 70 80 90 100
LLGTPGESTE EELLRRLQQI KEGPPPQSPD ENRAGESSDD VTNSDSIIDW
110 120 130 140 150
LNSVRQTGNT TRSGQRGNQS WRAVSRTNPN SGDFRFSLEI NVNRNNGSQT
160 170 180 190 200
SENESEPSTR RLSVENMESS SQRQMENSAS ESASARPSRA ERNSAEAVTE
210 220 230 240 250
VPTTRAQRRA RSRSPEHRRT RARAERSRSP LQPTSEIPRR APTLEQSSEN
260 270 280 290 300
EPEGSSRTRH HVTLRQQISG PELLGRGLFA ASGSRNPSQG TSSSDTGSNS
310 320 330 340 350
ESSGSGQRPP TIVLDLQVRR VRPGEYRQRD SIASRTRSRS QAPNNTVTYE
360 370 380 390 400
SERGGFRRTF SRSERAGVRT YVSTIRIPIR RILNTGLSET TSVAIQTMLR
410 420 430 440 450
QIMTGFGELS YFMYSDSDSE PSASVSSRNV ERVESRNGRG SSGGGNSSGS
460 470 480 490 500
SSSSSPSPSS SGESSESSSE MFEGSSEGGS SGPSRRDGRH RAPVTFDESG
510 520 530 540 550
SLPFLSLAQF FLLNEDDEDQ PRGLTKEQID NLAMRSFGEN DALKTCSVCI
560 570 580 590 600
TEYTEGNKLR KLPCSHEYHV HCIDRWLSEN STCPICRRAV LSSGNRESVV
Length:600
Mass (Da):66,377
Last modified:September 22, 2009 - v2
Checksum:i6BFB9958502FDAED
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti114G → R in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti146N → S in BAC26379 (PubMed:16141072).Curated1
Sequence conflicti195A → T in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti228R → M in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti320R → G in BAC26379 (PubMed:16141072).Curated1
Sequence conflicti362R → S in BAB28712 (PubMed:16141072).Curated1
Sequence conflicti470E → K in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti486R → K in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti505L → F in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti557N → D in AAD34209 (PubMed:10431247).Curated1
Sequence conflicti568Y → F in AAD34209 (PubMed:10431247).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF069992 mRNA Translation: AAD34209.1
AK013207 mRNA Translation: BAB28712.1
AK029295 mRNA Translation: BAC26379.1
AL805911 Genomic DNA Translation: CAM26768.1
CH466564 Genomic DNA Translation: EDL14089.1
CH466564 Genomic DNA Translation: EDL14090.1
BC012960 mRNA Translation: AAH12960.1
CCDSiCCDS30331.1
RefSeqiNP_035406.3, NM_011276.3
XP_006527981.1, XM_006527918.3
XP_006527982.1, XM_006527919.3
XP_006527983.1, XM_006527920.3
XP_006527984.1, XM_006527921.3
XP_011245853.1, XM_011247551.2
XP_011245854.1, XM_011247552.2
UniGeneiMm.427762
Mm.490660

Genome annotation databases

EnsembliENSMUST00000070705; ENSMUSP00000070662; ENSMUSG00000056537
ENSMUST00000121153; ENSMUSP00000112820; ENSMUSG00000056537
GeneIDi19820
KEGGimmu:19820
UCSCiuc009tzz.1 mouse

Similar proteinsi

Entry informationi

Entry nameiRNF12_MOUSE
AccessioniPrimary (citable) accession number: Q9WTV7
Secondary accession number(s): Q8CE02, Q91X19, Q9CYY2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 21, 2001
Last sequence update: September 22, 2009
Last modified: March 28, 2018
This is version 141 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

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