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Q99ML9

- RN111_MOUSE

UniProt

Q99ML9 - RN111_MOUSE

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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

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.2 Publications

Pathwayi

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri937 – 97842RING-type; atypical
Add
BLAST

GO - Molecular functioni

  1. SUMO polymer binding Source: UniProtKB
  2. ligase activity Source: UniProtKB-KW
  3. protein 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
Complete GO annotation...

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

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
Complete GO annotation...

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 Arkadia
PRO_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.1 Publication

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.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni240 – 402163Interaction with AXIN1 By similarity
Add
BLAST

Motif

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

Compositional bias

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

Sequence similaritiesi

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

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei909 – 9168Missing in isoform 2.
VSP_023842

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti121 – 1211L → V in BAC29394. 1 Publication
Sequence conflicti219 – 2191S → G in BAC33245. 1 Publication
Sequence conflicti256 – 2561S → N in BAC33245. 1 Publication
Sequence conflicti805 – 8051L → V in AAH54842. 1 Publication

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

« Hide 'large scale' publications
  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: September 3, 2014
This is version 112 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

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