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E3 ubiquitin-protein ligase RNF4 (EC 2.3.2.27) (RING finger protein 4) (RING-type E3 ubiquitin transferase RNF4) (Small nuclear ring finger protein) (Protein SNURF)

 RNF4_RAT                Reviewed;         194 AA.
O88846;
18-OCT-2001, integrated into UniProtKB/Swiss-Prot.
01-NOV-1998, sequence version 1.
18-JUL-2018, entry version 140.
RecName: Full=E3 ubiquitin-protein ligase RNF4;
EC=2.3.2.27;
AltName: Full=RING finger protein 4;
AltName: Full=RING-type E3 ubiquitin transferase RNF4 {ECO:0000305};
AltName: Full=Small nuclear ring finger protein;
Short=Protein SNURF;
Name=Rnf4; Synonyms=Snurf;
Rattus norvegicus (Rat).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Rattus.
NCBI_TaxID=10116;
[1]
NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, INTERACTION WITH AR AND TBP, AND
SUBCELLULAR LOCATION.
TISSUE=Testis;
PubMed=9710597; DOI=10.1128/MCB.18.9.5128;
Moilanen A.-M., Poukka H., Karvonen U., Hakli M., Janne O.A.,
Palvimo J.J.;
"Identification of a novel RING finger protein as a coregulator in
steroid receptor-mediated gene transcription.";
Mol. Cell. Biol. 18:5128-5139(1998).
[2]
NUCLEOTIDE SEQUENCE [MRNA].
STRAIN=Sprague-Dawley;
Yan W., Hirvonen S.J., Moilanen A.-M., Janne O.A., Palvimo J.J.,
Toppari J.;
"Analysis of androgen receptor coregulator SNURF/RNF4 expression in
rat testis.";
Submitted (AUG-2001) to the EMBL/GenBank/DDBJ databases.
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
TISSUE=Prostate;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
FUNCTION, MUTAGENESIS OF 8-ARG--ARG-11, AND SUBCELLULAR LOCATION.
PubMed=11319220; DOI=10.1074/jbc.M009891200;
Haekli M., Karvonen U., Jaenne O.A., Palvimo J.J.;
"The RING finger protein SNURF is a bifunctional protein possessing
DNA binding activity.";
J. Biol. Chem. 276:23653-23660(2001).
[5]
FUNCTION, AUTOUBIQUITINATION, AND MUTAGENESIS OF CYS-136; CYS-139;
CYS-177 AND CYS-180.
PubMed=14987998; DOI=10.1016/S0014-5793(04)00070-5;
Haekli M., Lorick K.L., Weissman A.M., Jaenne O.A., Palvimo J.J.;
"Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3
ligase activity.";
FEBS Lett. 560:56-62(2004).
[6]
FUNCTION, SUMOYLATION, AND INTERACTION WITH PML.
PubMed=15707587; DOI=10.1016/j.yexcr.2004.10.029;
Haekli M., Karvonen U., Jaenne O.A., Palvimo J.J.;
"SUMO-1 promotes association of SNURF (RNF4) with PML nuclear
bodies.";
Exp. Cell Res. 304:224-233(2005).
[7]
FUNCTION, AND MUTAGENESIS OF 40-ILE--VAL-43; 50-ILE--ASP-53;
61-VAL--VAL-63 AND 71-VAL--VAL-74.
PubMed=18408734; DOI=10.1038/ncb1716;
Tatham M.H., Geoffroy M.C., Shen L., Plechanovova A., Hattersley N.,
Jaffray E.G., Palvimo J.J., Hay R.T.;
"RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for
arsenic-induced PML degradation.";
Nat. Cell Biol. 10:538-546(2008).
[8]
FUNCTION, INTERACTION WITH SUMOYLATED PML, AND SUBCELLULAR LOCATION.
PubMed=20943951; DOI=10.1091/mbc.E10-05-0449;
Geoffroy M.C., Jaffray E.G., Walker K.J., Hay R.T.;
"Arsenic-induced SUMO-dependent recruitment of RNF4 into PML nuclear
bodies.";
Mol. Biol. Cell 21:4227-4239(2010).
[9]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-98 AND SER-99, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22673903; DOI=10.1038/ncomms1871;
Lundby A., Secher A., Lage K., Nordsborg N.B., Dmytriyev A.,
Lundby C., Olsen J.V.;
"Quantitative maps of protein phosphorylation sites across 14
different rat organs and tissues.";
Nat. Commun. 3:876-876(2012).
[10]
X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 124-194 IN COMPLEX WITH ZINC
IONS, DOMAIN, AND SUBUNIT.
PubMed=20681948; DOI=10.1042/BJ20100957;
Liew C.W., Sun H., Hunter T., Day C.L.;
"RING domain dimerization is essential for RNF4 function.";
Biochem. J. 431:23-29(2010).
-!- FUNCTION: 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. {ECO:0000269|PubMed:11319220,
ECO:0000269|PubMed:14987998, ECO:0000269|PubMed:15707587,
ECO:0000269|PubMed:18408734, ECO:0000269|PubMed:20943951,
ECO:0000269|PubMed:9710597}.
-!- CATALYTIC ACTIVITY: S-ubiquitinyl-[E2 ubiquitin-conjugating
enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-
conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor
protein]-L-lysine.
-!- PATHWAY: Protein modification; protein ubiquitination.
-!- SUBUNIT: Homodimer (via RING-type zinc finger domain). Interacts
with PATZ1 (By similarity). Interacts with TRPS1; negatively
regulates the TRPS1 transcriptional repressor activity (By
similarity). Interacts with GSC2 (By similarity). Interacts with
TCF20 (By similarity). Interacts with PARP1 (By similarity).
Interacts with AR/the androgen receptor and TBP. Interacts with
PML; SUMO1-dependent. Interacts with PML; SUMO2-dependent.
Interacts with PML (By similarity). {ECO:0000250}.
-!- INTERACTION:
Self; NbExp=4; IntAct=EBI-7258907, EBI-7258907;
P27695:APEX1 (xeno); NbExp=2; IntAct=EBI-7258907, EBI-1048805;
P61956:SUMO2 (xeno); NbExp=2; IntAct=EBI-7258907, EBI-473220;
Q13569:TDG (xeno); NbExp=2; IntAct=EBI-7258907, EBI-348333;
P51668:UBE2D1 (xeno); NbExp=4; IntAct=EBI-7258907, EBI-743540;
-!- SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Nucleus, PML body.
Nucleus, nucleoplasm.
-!- TISSUE SPECIFICITY: Widely expressed with highest levels in
testis.
-!- DOMAIN: The RING-type zinc finger domain is required for the
ubiquitination of polysumoylated substrates.
{ECO:0000269|PubMed:20681948}.
-!- DOMAIN: The SUMO interaction motifs (SIMs) mediates the binding to
polysumoylated substrate. {ECO:0000269|PubMed:18408734}.
-!- PTM: Sumoylated; conjugated by one or two SUMO1 moieties.
{ECO:0000269|PubMed:15707587}.
-!- PTM: Autoubiquitinated. {ECO:0000269|PubMed:14987998}.
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EMBL; AF022081; AAC35248.1; -; mRNA.
EMBL; AY050655; AAL06715.1; -; mRNA.
EMBL; BC062024; AAH62024.1; -; mRNA.
RefSeq; NP_062055.1; NM_019182.2.
RefSeq; XP_008768493.1; XM_008770271.2.
RefSeq; XP_008768494.1; XM_008770272.2.
RefSeq; XP_008768495.1; XM_008770273.2.
RefSeq; XP_017454634.1; XM_017599145.1.
RefSeq; XP_017454635.1; XM_017599146.1.
UniGene; Rn.30015; -.
PDB; 3NG2; X-ray; 1.80 A; A/B=124-194.
PDB; 4AP4; X-ray; 2.21 A; A=131-194.
PDB; 5AIT; X-ray; 3.40 A; A=131-194.
PDB; 5AIU; X-ray; 2.21 A; A=131-194.
PDBsum; 3NG2; -.
PDBsum; 4AP4; -.
PDBsum; 5AIT; -.
PDBsum; 5AIU; -.
ProteinModelPortal; O88846; -.
SMR; O88846; -.
BioGrid; 247945; 10.
IntAct; O88846; 12.
MINT; O88846; -.
STRING; 10116.ENSRNOP00000019555; -.
iPTMnet; O88846; -.
PhosphoSitePlus; O88846; -.
PaxDb; O88846; -.
PRIDE; O88846; -.
Ensembl; ENSRNOT00000019555; ENSRNOP00000019555; ENSRNOG00000013930.
GeneID; 29274; -.
KEGG; rno:29274; -.
CTD; 6047; -.
RGD; 3583; Rnf4.
eggNOG; KOG0320; Eukaryota.
eggNOG; ENOG410XV78; LUCA.
GeneTree; ENSGT00390000010318; -.
HOGENOM; HOG000059548; -.
HOVERGEN; HBG018577; -.
InParanoid; O88846; -.
KO; K22651; -.
PhylomeDB; O88846; -.
TreeFam; TF328387; -.
BRENDA; 6.3.2.19; 5301.
Reactome; R-RNO-983168; Antigen processing: Ubiquitination & Proteasome degradation.
UniPathway; UPA00143; -.
EvolutionaryTrace; O88846; -.
PRO; PR:O88846; -.
Proteomes; UP000002494; Chromosome 14.
Bgee; ENSRNOG00000013930; -.
ExpressionAtlas; O88846; baseline and differential.
Genevisible; O88846; RN.
GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
GO; GO:0005829; C:cytosol; IDA:RGD.
GO; GO:0005654; C:nucleoplasm; IDA:UniProtKB.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0016605; C:PML body; IEA:UniProtKB-SubCell.
GO; GO:0050681; F:androgen receptor binding; IPI:RGD.
GO; GO:0003677; F:DNA binding; IDA:UniProtKB.
GO; GO:0030331; F:estrogen receptor binding; IPI:RGD.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0031491; F:nucleosome binding; IDA:UniProtKB.
GO; GO:0033142; F:progesterone receptor binding; IPI:RGD.
GO; GO:0042803; F:protein homodimerization activity; IDA:RGD.
GO; GO:0032184; F:SUMO polymer binding; IDA:RGD.
GO; GO:0017025; F:TBP-class protein binding; IDA:RGD.
GO; GO:0031624; F:ubiquitin conjugating enzyme binding; IPI:RGD.
GO; GO:0061630; F:ubiquitin protein ligase activity; IDA:RGD.
GO; GO:0004842; F:ubiquitin-protein transferase activity; IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IDA:RGD.
GO; GO:0071243; P:cellular response to arsenic-containing substance; IEP:RGD.
GO; GO:0071345; P:cellular response to cytokine stimulus; IEP:RGD.
GO; GO:0071480; P:cellular response to gamma radiation; IMP:RGD.
GO; GO:0072711; P:cellular response to hydroxyurea; IMP:RGD.
GO; GO:0071394; P:cellular response to testosterone stimulus; IDA:RGD.
GO; GO:0008584; P:male gonad development; IEP:RGD.
GO; GO:0060548; P:negative regulation of cell death; IMP:RGD.
GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IDA:RGD.
GO; GO:0045893; P:positive regulation of transcription, DNA-templated; IDA:UniProtKB.
GO; GO:0043161; P:proteasome-mediated ubiquitin-dependent protein catabolic process; ISS:UniProtKB.
GO; GO:0051865; P:protein autoubiquitination; IDA:RGD.
GO; GO:0070979; P:protein K11-linked ubiquitination; IDA:UniProtKB.
GO; GO:0070936; P:protein K48-linked ubiquitination; IDA:UniProtKB.
GO; GO:0085020; P:protein K6-linked ubiquitination; IDA:UniProtKB.
GO; GO:0070534; P:protein K63-linked ubiquitination; IDA:UniProtKB.
GO; GO:0016567; P:protein ubiquitination; IMP:UniProtKB.
GO; GO:0090234; P:regulation of kinetochore assembly; ISS:UniProtKB.
GO; GO:0090169; P:regulation of spindle assembly; ISS:UniProtKB.
GO; GO:0046685; P:response to arsenic-containing substance; IDA:UniProtKB.
GO; GO:0032355; P:response to estradiol; IEP:RGD.
GO; GO:0044752; P:response to human chorionic gonadotropin; IEP:RGD.
GO; GO:0007283; P:spermatogenesis; IEP:RGD.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 3.30.40.10; -; 1.
InterPro; IPR001841; Znf_RING.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
InterPro; IPR017907; Znf_RING_CS.
Pfam; PF13639; zf-RING_2; 1.
SMART; SM00184; RING; 1.
PROSITE; PS00518; ZF_RING_1; 1.
PROSITE; PS50089; ZF_RING_2; 1.
1: Evidence at protein level;
3D-structure; Activator; Complete proteome; Cytoplasm; DNA-binding;
Metal-binding; Nucleus; Phosphoprotein; Reference proteome;
Transcription; Transcription regulation; Transferase; Ubl conjugation;
Ubl conjugation pathway; Zinc; Zinc-finger.
CHAIN 1 194 E3 ubiquitin-protein ligase RNF4.
/FTId=PRO_0000056045.
ZN_FING 136 181 RING-type. {ECO:0000255|PROSITE-
ProRule:PRU00175}.
REGION 1 20 Required for ubiquitination activity.
{ECO:0000250}.
REGION 6 65 Mediates interaction with TRPS1.
{ECO:0000250}.
MOTIF 40 43 SUMO interaction motif 1.
{ECO:0000269|PubMed:18408734}.
MOTIF 50 53 SUMO interaction motif 2.
{ECO:0000269|PubMed:18408734}.
MOTIF 61 63 SUMO interaction motif 3.
{ECO:0000269|PubMed:18408734}.
MOTIF 71 74 SUMO interaction motif 4.
{ECO:0000269|PubMed:18408734}.
MOD_RES 98 98 Phosphoserine.
{ECO:0000244|PubMed:22673903}.
MOD_RES 99 99 Phosphoserine.
{ECO:0000244|PubMed:22673903}.
MUTAGEN 8 11 RKRR->AAAA: Altered DNA-binding activity.
{ECO:0000269|PubMed:11319220}.
MUTAGEN 40 43 IELV->AEAA: No effect. Loss of binding
and ubiquitination of poly-SUMO chains;
when associated with 50-A--A-53; 61-A--A-
63 and 71-A--A-74.
{ECO:0000269|PubMed:18408734}.
MUTAGEN 50 53 IVDL->AADA: Alters binding to poly-SUMO
chains. Loss of binding and
ubiquitination of poly-SUMO chains; when
associated with 40-A--A-43; 61-A--A-63
and 71-A--A-74.
{ECO:0000269|PubMed:18408734}.
MUTAGEN 61 63 VVV->AAA: No effect. Loss of binding and
ubiquitination of poly-SUMO chains; when
associated with 40-A--A-43; 50-A--A-53
and 71-A--A-74.
{ECO:0000269|PubMed:18408734}.
MUTAGEN 71 74 VVIV->AAAA: No effect. Loss of binding
and ubiquitination of poly-SUMO chains;
when associated with 40-A--A-43; 50-A--A-
53 and 61-A--A-63.
{ECO:0000269|PubMed:18408734}.
MUTAGEN 136 136 C->S: Loss of ubiquitination activity;
when associated with S-139.
{ECO:0000269|PubMed:14987998}.
MUTAGEN 139 139 C->S: Loss of ubiquitination activity;
when associated with S-136.
{ECO:0000269|PubMed:14987998}.
MUTAGEN 177 177 C->S: Loss of ubiquitination activity;
when associated with S-180.
{ECO:0000269|PubMed:14987998}.
MUTAGEN 180 180 C->S: Loss of ubiquitination activity;
when associated with S-177.
{ECO:0000269|PubMed:14987998}.
TURN 137 139 {ECO:0000244|PDB:3NG2}.
HELIX 143 147 {ECO:0000244|PDB:3NG2}.
TURN 148 150 {ECO:0000244|PDB:3NG2}.
STRAND 153 155 {ECO:0000244|PDB:3NG2}.
STRAND 161 163 {ECO:0000244|PDB:3NG2}.
HELIX 164 173 {ECO:0000244|PDB:3NG2}.
TURN 178 180 {ECO:0000244|PDB:3NG2}.
STRAND 189 193 {ECO:0000244|PDB:4AP4}.
SEQUENCE 194 AA; 21897 MW; 40C13970FC11DFF2 CRC64;
MSTRNPQRKR RGGAVNSRQT QKRTRETTST PEISLEAEPI ELVETVGDEI VDLTCESLEP
VVVDLTHNDS VVIVEERRRP RRNGRRLRQD HADSCVVSSD DEELSKDKDV YVTTHTPRST
KDEGTTGLRP SGTVSCPICM DGYSEIVQNG RLIVSTECGH VFCSQCLRDS LKNANTCPTC
RKKINHKRYH PIYI


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