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Protein

E3 ubiquitin-protein ligase RNF4

Gene

Rnf4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

E3 ubiquitin-protein ligase which binds polysumoylated chains covalently attached to proteins and mediates 'Lys-6'-, 'Lys-11'-, 'Lys-48'- and 'Lys-63'-linked polyubiquitination of those substrates and their subsequent targeting to the proteasome for degradation. Regulates the degradation of several proteins including PML and the transcriptional activator PEA3. Involved in chromosome alignment and spindle assembly, it regulates the kinetochore CENPH-CENPI-CENPK complex by targeting polysumoylated CENPI to proteasomal degradation. Regulates the cellular responses to hypoxia and heat shock through degradation of respectively EPAS1 and PARP1. Alternatively, it may also bind DNA/nucleosomes and have a more direct role in the regulation of transcription for instance enhancing basal transcription and steroid receptor-mediated transcriptional activation.1 Publication

Pathwayi

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri136 – 18146RING-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB
  2. ligase activity Source: UniProtKB-KW
  3. nucleosome binding Source: UniProtKB
  4. SUMO polymer binding Source: UniProtKB
  5. transcription factor binding Source: MGI
  6. ubiquitin-protein transferase activity Source: UniProtKB
  7. zinc ion binding Source: InterPro

GO - Biological processi

  1. positive regulation of transcription, DNA-templated Source: UniProtKB
  2. positive regulation of transcription from RNA polymerase II promoter Source: UniProtKB
  3. proteasome-mediated ubiquitin-dependent protein catabolic process Source: UniProtKB
  4. protein autoubiquitination Source: UniProtKB
  5. protein K11-linked ubiquitination Source: UniProtKB
  6. protein K48-linked ubiquitination Source: UniProtKB
  7. protein K63-linked ubiquitination Source: UniProtKB
  8. protein K6-linked ubiquitination Source: UniProtKB
  9. regulation of kinetochore assembly Source: UniProtKB
  10. regulation of spindle assembly Source: UniProtKB
  11. response to arsenic-containing substance Source: MGI
  12. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Ligase

Keywords - Biological processi

Transcription, Transcription regulation, Ubl conjugation pathway

Keywords - Ligandi

DNA-binding, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiREACT_199115. Antigen processing: Ubiquitination & Proteasome degradation.
UniPathwayiUPA00143.

Names & Taxonomyi

Protein namesi
Recommended name:
E3 ubiquitin-protein ligase RNF4 (EC:6.3.2.-)
Alternative name(s):
RING finger protein 4
Gene namesi
Name:Rnf4
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 5

Organism-specific databases

MGIiMGI:1201691. Rnf4.

Subcellular locationi

Cytoplasm. Nucleus. NucleusPML body By similarity. Nucleusnucleoplasm By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB
  2. nucleus Source: UniProtKB
  3. PML body Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi134 – 1341V → E: Abolishes homodimerization. Strongly reduced E3 ubiquitin ligase activity. 1 Publication
Mutagenesisi155 – 1551S → A: No effect. 1 Publication
Mutagenesisi155 – 1551S → E: Abolishes homodimerization. Strongly reduced E3 ubiquitin ligase activity. 1 Publication
Mutagenesisi161 – 1611V → A: Abolishes homodimerization. Strongly reduced E3 ubiquitin ligase activity. 1 Publication
Mutagenesisi193 – 1931Y → A: Abolishes homodimerization. Loss of E3 ubiquitin ligase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 194194E3 ubiquitin-protein ligase RNF4PRO_0000056044Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei98 – 981Phosphoserine1 Publication
Modified residuei99 – 991PhosphoserineBy similarity

Post-translational modificationi

Sumoylated; conjugated by one or two SUMO1 moieties.By similarity
Autoubiquitinated.1 Publication

Keywords - PTMi

Phosphoprotein, Ubl conjugation

Proteomic databases

PRIDEiQ9QZS2.

PTM databases

PhosphoSiteiQ9QZS2.

Miscellaneous databases

PMAP-CutDBQ9QZS2.

Expressioni

Tissue specificityi

In the embryo, expressed primarily in the developing nervous system with strong expression in the dorsal root ganglia and gonads. Ubiquitously expressed in the adult.

Developmental stagei

Expression is detected from embryonic day 7 and continues throughout development and into adulthood.

Gene expression databases

BgeeiQ9QZS2.
CleanExiMM_RNF4.
ExpressionAtlasiQ9QZS2. baseline and differential.
GenevestigatoriQ9QZS2.

Interactioni

Subunit structurei

Homodimer (via RING-type zinc finger domain). Interacts with AR/the androgen receptor and TBP (By similarity). Interacts with PATZ1 (By similarity). Interacts with PML; SUMO1-dependent. Interacts with PML; SUMO2-dependent (By similarity). Interacts with TRPS1; negatively regulates the TRPS1 transcriptional repressor activity. Interacts with GSC2. Interacts with TCF20. Interacts with PARP1. Interacts with PML (By similarity).By similarity

Protein-protein interaction databases

BioGridi202920. 3 interactions.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MP2NMR-C45-69[»]
ProteinModelPortaliQ9QZS2.
SMRiQ9QZS2. Positions 129-194.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1 – 2020Required for ubiquitination activityAdd
BLAST
Regioni6 – 6560Mediates interaction with TRPS1Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi40 – 434SUMO interaction motif 1; mediates the binding to polysumoylated substrates
Motifi50 – 534SUMO interaction motif 2; mediates the binding to polysumoylated substrates
Motifi61 – 633SUMO interaction motif 3; mediates the binding to polysumoylated substrates
Motifi71 – 744SUMO interaction motif 4; mediates the binding to polysumoylated substrates

Domaini

The RING-type zinc finger domain is required for the ubiquitination.By similarity

Sequence similaritiesi

Contains 1 RING-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri136 – 18146RING-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiNOG327779.
GeneTreeiENSGT00390000010318.
HOVERGENiHBG018577.
InParanoidiQ9QZS2.
OMAiTHRQYHP.
OrthoDBiEOG7SN8F1.
PhylomeDBiQ9QZS2.
TreeFamiTF328387.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9QZS2-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTRNPQRKR RGGTVNSRQT QKRTRETTST PEVSLETEPI ELVETVGDEI
60 70 80 90 100
VDLTCESLEP VVVDLTHNDS VVIVEERRRP RRNGRRLRQD HADSCVVSSD
110 120 130 140 150
DEELSRDKDV YVTTHTPRST KDDGATGPRP SGTVSCPICM DGYSEIVQNG
160 170 180 190
RLIVSTECGH VFCSQCLRDS LKNANTCPTC RKKINHKRYH PIYI
Length:194
Mass (Da):21,911
Last modified:May 1, 2000 - v1
Checksum:i9A0A4277725C62E5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169300 mRNA. Translation: AAF00620.1.
AK019171 mRNA. Translation: BAB31585.1.
AK090162 mRNA. Translation: BAC41119.1.
AK147057 mRNA. Translation: BAE27641.1.
AK151116 mRNA. Translation: BAE30125.1.
AK158987 mRNA. Translation: BAE34757.1.
AK159778 mRNA. Translation: BAE35362.1.
AK159949 mRNA. Translation: BAE35505.1.
BC003282 mRNA. Translation: AAH03282.1.
U95141 mRNA. Translation: AAC53539.1.
CCDSiCCDS57336.1.
RefSeqiNP_035408.1. NM_011278.5.
XP_006503868.1. XM_006503805.1.
UniGeneiMm.21281.

Genome annotation databases

EnsembliENSMUST00000030992; ENSMUSP00000030992; ENSMUSG00000029110.
ENSMUST00000182047; ENSMUSP00000138411; ENSMUSG00000029110.
ENSMUST00000182709; ENSMUSP00000138555; ENSMUSG00000029110.
GeneIDi19822.
KEGGimmu:19822.
UCSCiuc008xcc.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF169300 mRNA. Translation: AAF00620.1.
AK019171 mRNA. Translation: BAB31585.1.
AK090162 mRNA. Translation: BAC41119.1.
AK147057 mRNA. Translation: BAE27641.1.
AK151116 mRNA. Translation: BAE30125.1.
AK158987 mRNA. Translation: BAE34757.1.
AK159778 mRNA. Translation: BAE35362.1.
AK159949 mRNA. Translation: BAE35505.1.
BC003282 mRNA. Translation: AAH03282.1.
U95141 mRNA. Translation: AAC53539.1.
CCDSiCCDS57336.1.
RefSeqiNP_035408.1. NM_011278.5.
XP_006503868.1. XM_006503805.1.
UniGeneiMm.21281.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MP2NMR-C45-69[»]
ProteinModelPortaliQ9QZS2.
SMRiQ9QZS2. Positions 129-194.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi202920. 3 interactions.

PTM databases

PhosphoSiteiQ9QZS2.

Proteomic databases

PRIDEiQ9QZS2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030992; ENSMUSP00000030992; ENSMUSG00000029110.
ENSMUST00000182047; ENSMUSP00000138411; ENSMUSG00000029110.
ENSMUST00000182709; ENSMUSP00000138555; ENSMUSG00000029110.
GeneIDi19822.
KEGGimmu:19822.
UCSCiuc008xcc.1. mouse.

Organism-specific databases

CTDi6047.
MGIiMGI:1201691. Rnf4.

Phylogenomic databases

eggNOGiNOG327779.
GeneTreeiENSGT00390000010318.
HOVERGENiHBG018577.
InParanoidiQ9QZS2.
OMAiTHRQYHP.
OrthoDBiEOG7SN8F1.
PhylomeDBiQ9QZS2.
TreeFamiTF328387.

Enzyme and pathway databases

UniPathwayiUPA00143.
ReactomeiREACT_199115. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

ChiTaRSiRnf4. mouse.
NextBioi297289.
PMAP-CutDBQ9QZS2.
PROiQ9QZS2.
SOURCEiSearch...

Gene expression databases

BgeeiQ9QZS2.
CleanExiMM_RNF4.
ExpressionAtlasiQ9QZS2. baseline and differential.
GenevestigatoriQ9QZS2.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR001841. Znf_RING.
IPR013083. Znf_RING/FYVE/PHD.
IPR017907. Znf_RING_CS.
[Graphical view]
PfamiPF13639. zf-RING_2. 1 hit.
[Graphical view]
SMARTiSM00184. RING. 1 hit.
[Graphical view]
PROSITEiPS00518. ZF_RING_1. 1 hit.
PS50089. ZF_RING_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Rnf4, a RING protein expressed in the developing nervous and reproductive systems, interacts with Gscl, a gene within the DiGeorge critical region."
    Galili N., Nayak S., Epstein J.A., Buck C.A.
    Dev. Dyn. 218:102-111(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], INTERACTION WITH GSC2.
    Strain: CD-1.
    Tissue: Embryo.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Bone marrow, Embryo, Kidney, Lymph node and Visual cortex.
  3. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "Identification and characterization of a novel RING-finger gene (RNF4) mapping at 4p16.3."
    Chiariotti L., Benvenuto G., Fedele M., Santoro M., Simeone A., Fusco A., Bruni C.B.
    Genomics 47:258-265(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 16-178.
    Tissue: Embryo.
  5. "Interaction between the transcription factor SPBP and the positive cofactor RNF4. An interplay between protein binding zinc fingers."
    Lyngsoe C., Bouteiller G., Damgaard C.K., Ryom D., Sanchez-Munoz S., Noerby P.L., Bonven B.J., Joergensen P.
    J. Biol. Chem. 275:26144-26149(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TCF20.
  6. "The RING finger protein RNF4, a co-regulator of transcription, interacts with the TRPS1 transcription factor."
    Kaiser F.J., Moeroey T., Chang G.T., Horsthemke B., Luedecke H.J.
    J. Biol. Chem. 278:38780-38785(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH TRPS1.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  8. "PARP-1 transcriptional activity is regulated by sumoylation upon heat shock."
    Martin N., Schwamborn K., Schreiber V., Werner A., Guillier C., Zhang X.D., Bischof O., Seeler J.S., Dejean A.
    EMBO J. 28:3534-3548(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH PARP1.
  9. "RING domain dimerization is essential for RNF4 function."
    Liew C.W., Sun H., Hunter T., Day C.L.
    Biochem. J. 431:23-29(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, AUTOUBIQUITINATION, MUTAGENESIS OF VAL-134; SER-155; VAL-161 AND TYR-193, SUBUNIT.

Entry informationi

Entry nameiRNF4_MOUSE
AccessioniPrimary (citable) accession number: Q9QZS2
Secondary accession number(s): O35941, Q541Z6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 18, 2001
Last sequence update: May 1, 2000
Last modified: March 4, 2015
This is version 122 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.