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Q99ML9

- RN111_MOUSE

UniProt

Q99ML9 - RN111_MOUSE

Protein

E3 ubiquitin-protein ligase Arkadia

Gene

Rnf111

Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 1 (01 Jun 2001)
      Previous versions | rss
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    Functioni

    Acts in the Nodal pathway of mesoderm patterning during embryonic development. Acts downstream AXIN1 as an E3 ubiquitin-protein ligase which promotes the ubiquitination of inhibitory SMADs such as SMAD7, induces their proteasomal degradation and thereby enhances the transcriptional activity of TGF-beta and BMP. Activates Smad3/Smad4-dependent transcription by triggering signal-induced SnoN degradation. Associates with UBE2D2 as an E2 enzyme By similarity.By similarity

    Pathwayi

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri937 – 97842RING-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ligase activity Source: UniProtKB-KW
    2. protein binding Source: UniProtKB
    3. SUMO polymer binding Source: UniProtKB
    4. ubiquitin-protein transferase activity Source: BHF-UCL
    5. zinc ion binding Source: InterPro

    GO - Biological processi

    1. pattern specification process Source: MGI
    2. positive regulation of protein ubiquitination Source: MGI
    3. positive regulation of transcription, DNA-templated Source: BHF-UCL
    4. positive regulation of transforming growth factor beta receptor signaling pathway Source: MGI
    5. protein polyubiquitination Source: BHF-UCL
    6. ubiquitin-dependent SMAD protein catabolic process Source: BHF-UCL

    Keywords - Molecular functioni

    Developmental protein, Ligase

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiREACT_199115. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_203903. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
    REACT_220566. Downregulation of SMAD2/3:SMAD4 transcriptional activity.
    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    E3 ubiquitin-protein ligase Arkadia (EC:6.3.2.-)
    Alternative name(s):
    RING finger protein 111
    Gene namesi
    Name:Rnf111
    OrganismiMus musculus (Mouse)
    Taxonomic identifieri10090 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
    ProteomesiUP000000589: Chromosome 9

    Organism-specific databases

    MGIiMGI:1934919. Rnf111.

    Subcellular locationi

    Nucleus 1 Publication. Cytoplasm By similarity
    Note: Upon TGF-beta treatment, translocates from nucleus to cytosol.By similarity

    GO - Cellular componenti

    1. cytoplasm Source: BHF-UCL
    2. nucleolus Source: Ensembl
    3. nucleoplasm Source: Reactome
    4. nucleus Source: BHF-UCL
    5. protein complex Source: MGI

    Keywords - Cellular componenti

    Cytoplasm, Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Mice rarely develop beyond 15 somites, have a reduced head, fail to undergo turning and die at midgestation.1 Publication

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi937 – 9371C → A: No effect on TGF-beta and BMP signaling. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 989989E3 ubiquitin-protein ligase ArkadiaPRO_0000280691Add
    BLAST

    Proteomic databases

    PRIDEiQ99ML9.

    PTM databases

    PhosphoSiteiQ99ML9.

    Expressioni

    Tissue specificityi

    Ubiquitously expressed.1 Publication

    Developmental stagei

    Ubiquitously expressed from ES cells to midgestation.1 Publication

    Gene expression databases

    BgeeiQ99ML9.
    CleanExiMM_RNF111.
    GenevestigatoriQ99ML9.

    Interactioni

    Subunit structurei

    Interacts with AXIN1 and AXIN2. Part of a complex containing RNF111, AXIN1 and SMAD7 By similarity. Interacts with SMAD6 and SMAD7. Interacts with SKIL isoform 1 By similarity. Interacts (via SIM domains) with SUMO1 and SUMO2 By similarity.By similarity

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    AXIN1O151695EBI-646015,EBI-710484From a different organism.
    Axin1O356254EBI-646015,EBI-2365912
    SMAD7O151052EBI-646015,EBI-3861591From a different organism.

    Protein-protein interaction databases

    BioGridi220311. 10 interactions.
    IntActiQ99ML9. 7 interactions.
    MINTiMINT-1899537.

    Structurei

    3D structure databases

    ProteinModelPortaliQ99ML9.
    SMRiQ99ML9. Positions 936-989.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni240 – 402163Interaction with AXIN1By similarityAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi298 – 3025SUMO interaction motif 1 (SIM); mediates the binding to polysumoylated substratesBy similarity
    Motifi323 – 3297SUMO interaction motif 2 (SIM); mediates the binding to polysumoylated substratesBy similarity
    Motifi380 – 3845SUMO interaction motif 3 (SIM); mediates the binding to polysumoylated substratesBy similarity

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi218 – 2214Poly-Ser
    Compositional biasi250 – 451202Ser-richAdd
    BLAST
    Compositional biasi492 – 52130His-richAdd
    BLAST
    Compositional biasi624 – 776153Pro-richAdd
    BLAST

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri937 – 97842RING-type; atypicalPROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG291583.
    GeneTreeiENSGT00730000110863.
    HOGENOMiHOG000154152.
    HOVERGENiHBG093884.
    InParanoidiQ99ML9.
    KOiK10635.
    OMAiPCRKRFV.
    OrthoDBiEOG7WHH9N.
    PhylomeDBiQ99ML9.
    TreeFamiTF331862.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR029306. RNF111_N.
    IPR001841. Znf_RING.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF15303. RNF111_N. 1 hit.
    PF13639. zf-RING_2. 1 hit.
    [Graphical view]
    SMARTiSM00184. RING. 1 hit.
    [Graphical view]
    PROSITEiPS50089. ZF_RING_2. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q99ML9-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MSQWTPEFNE LYTLKVAMKS GTPDAPTTQE SLKAVLLHPQ PLGATKSFPA    50
    EVEMINSKVG NEFSHLCDDS QKQEKDMTGN QQEQEKSGVV RKKRKSQQAG 100
    PSYVQNCVKE NQEILGRRQQ LETPSDEDND SSLSECLSSP SSSLHFGGSD 150
    TVTSDEDKEV SVRHTQPVLS AKSRSHSARS HKWPRTEADP VPSLLMKRPC 200
    FHGSALRRVT CRKRLVKSSS SQRTQKQKER MLVQRKKREA LAQRKYALLS 250
    SSSSSSENDL SSDSSSSSST DGEEDLCASA SENPSNPAAP SGSIDEDVVV 300
    IEASFTPQVT ANEEINVTST DSEVEIVTVG ESYRSRSTLG HSRSHWSQGS 350
    SSHTGRPQES RNRSRISTVI QPLRQNAAEV VDLTVDEDEP TIVPTTSARM 400
    DSQTTSASIN NSNPSTSEQA SDTTSTVASS QPSTVSETEA TLTSNSATGS 450
    SVGDDVRRTA SSAVPESGPP AMPRLPSCCP QHSPCGGTSQ SHHALAHPHS 500
    SCFQQHGHHF QHHHHHHHTP HPAVPVSPSF SDPACPVERP QVQAPCGANS 550
    SSGSSYHDQQ ALPVDLSNSA LRTHGSGGFH GASAFDPCCP VTSSRAAVFG 600
    HQAAAAPTQP LSIDGYGSSM VAQPQPQPPP QPSLSSCRHY MPPPYASLTR 650
    PLHHQASACH HSHGNAPPQT QPPPQVDYVI PHPVHAFHSQ ISSHAASHPV 700
    APPPPTHLGS TAAPIPQHLP PAHQPISHHI PAPAPSAQRL HPHEVMQRME 750
    VQRRRMMQHP TRAHERPPPH PHRMHPNYGH GHHIHVPQTM SSHPRQAPER 800
    TAWELGIEAG VTAATYTPGA LHPHLAHYHA PPRLHHLQLG ALPLMVPDMA 850
    GYPHIRYISS GLDGASFRGP FRGNFEELIH LEERLGNVNR GASQGTIERC 900
    TYPHKYKKVT TDWFSQRKLH CKQDGEEGTE EDTEEKCTIC LSILEEGEDV 950
    RRLPCMHLFH QVCVDQWLIT NKKCPICRVD IEAQLPSES 989
    Length:989
    Mass (Da):107,896
    Last modified:June 1, 2001 - v1
    Checksum:i212E3C37BC70DCB5
    GO
    Isoform 2 (identifier: Q99ML9-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         909-916: Missing.

    Show »
    Length:981
    Mass (Da):106,931
    Checksum:i4BC421580AB2ACEB
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti121 – 1211L → V in BAC29394. (PubMed:16141072)Curated
    Sequence conflicti219 – 2191S → G in BAC33245. (PubMed:16141072)Curated
    Sequence conflicti256 – 2561S → N in BAC33245. (PubMed:16141072)Curated
    Sequence conflicti805 – 8051L → V in AAH54842. (PubMed:15489334)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei909 – 9168Missing in isoform 2. 2 PublicationsVSP_023842

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF330197 mRNA. Translation: AAK38272.1.
    AK048110 mRNA. Translation: BAC33245.1.
    AK036351 mRNA. Translation: BAC29394.1.
    AK137148 mRNA. Translation: BAE23252.1.
    BC054842 mRNA. Translation: AAH54842.1.
    BC069835 mRNA. Translation: AAH69835.1.
    CCDSiCCDS23321.1. [Q99ML9-1]
    RefSeqiNP_291082.1. NM_033604.2. [Q99ML9-1]
    XP_006511648.1. XM_006511585.1. [Q99ML9-2]
    XP_006511649.1. XM_006511586.1. [Q99ML9-2]
    UniGeneiMm.29783.

    Genome annotation databases

    EnsembliENSMUST00000034739; ENSMUSP00000034739; ENSMUSG00000032217. [Q99ML9-1]
    ENSMUST00000113595; ENSMUSP00000109225; ENSMUSG00000032217. [Q99ML9-1]
    GeneIDi93836.
    KEGGimmu:93836.
    UCSCiuc009qoa.1. mouse. [Q99ML9-2]
    uc009qoe.1. mouse. [Q99ML9-1]

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF330197 mRNA. Translation: AAK38272.1 .
    AK048110 mRNA. Translation: BAC33245.1 .
    AK036351 mRNA. Translation: BAC29394.1 .
    AK137148 mRNA. Translation: BAE23252.1 .
    BC054842 mRNA. Translation: AAH54842.1 .
    BC069835 mRNA. Translation: AAH69835.1 .
    CCDSi CCDS23321.1. [Q99ML9-1 ]
    RefSeqi NP_291082.1. NM_033604.2. [Q99ML9-1 ]
    XP_006511648.1. XM_006511585.1. [Q99ML9-2 ]
    XP_006511649.1. XM_006511586.1. [Q99ML9-2 ]
    UniGenei Mm.29783.

    3D structure databases

    ProteinModelPortali Q99ML9.
    SMRi Q99ML9. Positions 936-989.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 220311. 10 interactions.
    IntActi Q99ML9. 7 interactions.
    MINTi MINT-1899537.

    PTM databases

    PhosphoSitei Q99ML9.

    Proteomic databases

    PRIDEi Q99ML9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENSMUST00000034739 ; ENSMUSP00000034739 ; ENSMUSG00000032217 . [Q99ML9-1 ]
    ENSMUST00000113595 ; ENSMUSP00000109225 ; ENSMUSG00000032217 . [Q99ML9-1 ]
    GeneIDi 93836.
    KEGGi mmu:93836.
    UCSCi uc009qoa.1. mouse. [Q99ML9-2 ]
    uc009qoe.1. mouse. [Q99ML9-1 ]

    Organism-specific databases

    CTDi 54778.
    MGIi MGI:1934919. Rnf111.

    Phylogenomic databases

    eggNOGi NOG291583.
    GeneTreei ENSGT00730000110863.
    HOGENOMi HOG000154152.
    HOVERGENi HBG093884.
    InParanoidi Q99ML9.
    KOi K10635.
    OMAi PCRKRFV.
    OrthoDBi EOG7WHH9N.
    PhylomeDBi Q99ML9.
    TreeFami TF331862.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .
    Reactomei REACT_199115. Antigen processing: Ubiquitination & Proteasome degradation.
    REACT_203903. SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription.
    REACT_220566. Downregulation of SMAD2/3:SMAD4 transcriptional activity.

    Miscellaneous databases

    NextBioi 351685.
    PROi Q99ML9.
    SOURCEi Search...

    Gene expression databases

    Bgeei Q99ML9.
    CleanExi MM_RNF111.
    Genevestigatori Q99ML9.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR029306. RNF111_N.
    IPR001841. Znf_RING.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    Pfami PF15303. RNF111_N. 1 hit.
    PF13639. zf-RING_2. 1 hit.
    [Graphical view ]
    SMARTi SM00184. RING. 1 hit.
    [Graphical view ]
    PROSITEi PS50089. ZF_RING_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Induction of the mammalian node requires Arkadia function in the extraembryonic lineages."
      Episkopou V., Arkell R., Timmons P.M., Walsh J.J., Andrew R.L., Swan D.
      Nature 410:825-830(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY, DEVELOPMENTAL STAGE, DISRUPTION PHENOTYPE.
      Strain: 129/Sv.
    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] (ISOFORM 2).
      Strain: C57BL/6J.
      Tissue: Cerebellum, Head and Urinary bladder.
    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] (ISOFORM 2), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 805-989 (ISOFORM 1).
      Strain: CD-1 and FVB/N-3.
      Tissue: Mammary tumor and Neural stem cell.
    4. "Arkadia amplifies TGF-beta superfamily signaling through degradation of Smad7."
      Koinuma D., Shinozaki M., Komuro A., Goto K., Saitoh M., Hanyu A., Ebina M., Nukiwa T., Miyazawa K., Imamura T., Miyazono K.
      EMBO J. 22:6458-6470(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF CYS-937, INTERACTION WITH SMAD6 AND SMAD7, SUBCELLULAR LOCATION.

    Entry informationi

    Entry nameiRN111_MOUSE
    AccessioniPrimary (citable) accession number: Q99ML9
    Secondary accession number(s): Q3UVL7
    , Q6NSW2, Q7TMR3, Q8C881, Q8CBC0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 20, 2007
    Last sequence update: June 1, 2001
    Last modified: October 1, 2014
    This is version 113 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

    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

    External Data

    Dasty 3