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P40318

- DOA10_YEAST

UniProt

P40318 - DOA10_YEAST

Protein

ERAD-associated E3 ubiquitin-protein ligase DOA10

Gene

SSM4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    E3 ubiquitin-protein ligase which accepts ubiquitin specifically from endoplasmic reticulum-associated UBC6 and UBC7 E2 ligases, and transfers it to substrates promoting their degradation. Mediates the degradation of a broad range of substrates, inluding endoplasmic reticulum membrane proteins (ERQC), soluble nuclear proteins and soluble cytoplasmic proteins (CytoQC). Component of the DOA10 ubiquitin ligase complex, which is part of the ERAD-C pathway responsible for the rapid degradation of membrane proteins with misfolded cytoplasmic domains. ERAD-C substrates are ubiquitinated through DOA10 in conjunction with the E2 ubiquitin-conjugating enzymes UBC6 and UBC7-CUE1. Ubiquitinated substrates are then removed to the cytosol via the action of the UFD1-NPL4-CDC48/p97 (UNC) AAA ATPase complex and targeted to the proteasome. Also recognizes the N-terminally acetylated residue of proteins as degradation signal (degron). N-terminally acetylated target proteins include MATALPHA2, TBF1, SLK19, YMR090W, HIS3, HSP104, UBP6 and ARO8.7 Publications

    Pathwayi

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri31 – 10070RING-CH-typePROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. ligase activity Source: UniProtKB-KW
    2. protein binding Source: IntAct
    3. ubiquitin-protein transferase activity Source: SGD
    4. zinc ion binding Source: InterPro

    GO - Biological processi

    1. ER-associated ubiquitin-dependent protein catabolic process Source: SGD

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Ubl conjugation pathway

    Keywords - Ligandi

    Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:G3O-31303-MONOMER.
    UniPathwayiUPA00143.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    ERAD-associated E3 ubiquitin-protein ligase DOA10 (EC:6.3.2.-)
    Gene namesi
    Name:SSM4
    Synonyms:DOA10
    Ordered Locus Names:YIL030C
    ORF Names:YI3299.01C, YI9905.18C
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome IX

    Organism-specific databases

    CYGDiYIL030c.
    SGDiS000001292. SSM4.

    Subcellular locationi

    GO - Cellular componenti

    1. Doa10p ubiquitin ligase complex Source: SGD
    2. integral component of endoplasmic reticulum membrane Source: SGD
    3. nuclear envelope Source: SGD
    4. nuclear inner membrane Source: SGD

    Keywords - Cellular componenti

    Endoplasmic reticulum, Membrane, Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 13191319ERAD-associated E3 ubiquitin-protein ligase DOA10PRO_0000072214Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei1 – 11N-acetylmethionine1 Publication

    Keywords - PTMi

    Acetylation

    Proteomic databases

    MaxQBiP40318.
    PaxDbiP40318.
    PeptideAtlasiP40318.

    Expressioni

    Gene expression databases

    GenevestigatoriP40318.

    Interactioni

    Subunit structurei

    Component of the DOA10 complex which contains SSM4/DOA10, CDC48, NPL4, UFD1 AND UBX2/SEL1. The complex is composed of the membrane integral E3 ligase SSM4/DOA10 and the heterotrimeric UFD1-NPL4-CDC48/p97 (UNC) ATPase complex recruited by UBX2/SEL1. Interacts with UBX2/SEL1. Interacts also with its associated ubiquitin conjugating enzymesh UBC6 and UBC7 with its membrane anchor CUE1. Interacts with PEX29.4 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    CDC48P256944EBI-18208,EBI-4308
    CUE1P384282EBI-18208,EBI-27580
    STE6P128662EBI-18208,EBI-18383
    UBX2Q042285EBI-18208,EBI-27730

    Protein-protein interaction databases

    BioGridi34959. 166 interactions.
    DIPiDIP-7286N.
    IntActiP40318. 81 interactions.
    MINTiMINT-1361830.
    STRINGi4932.YIL030C.

    Structurei

    Secondary structure

    1
    1319
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi40 – 423
    Beta strandi48 – 503
    Helixi67 – 7610
    Beta strandi91 – 933

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2M6MNMR-A19-101[»]
    ProteinModelPortaliP40318.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini1 – 131131CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini153 – 20351LumenalSequence AnalysisAdd
    BLAST
    Topological domaini225 – 468244CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini490 – 4912LumenalSequence Analysis
    Topological domaini513 – 626114CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini648 – 66013LumenalSequence AnalysisAdd
    BLAST
    Topological domaini682 – 73958CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini761 – 77717LumenalSequence AnalysisAdd
    BLAST
    Topological domaini798 – 965168CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini987 – 101933LumenalSequence AnalysisAdd
    BLAST
    Topological domaini1041 – 111373CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini1135 – 116834LumenalSequence AnalysisAdd
    BLAST
    Topological domaini1190 – 121324CytoplasmicSequence AnalysisAdd
    BLAST
    Topological domaini1235 – 127036LumenalSequence AnalysisAdd
    BLAST
    Topological domaini1292 – 131928CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei132 – 15221HelicalSequence AnalysisAdd
    BLAST
    Transmembranei204 – 22421HelicalSequence AnalysisAdd
    BLAST
    Transmembranei469 – 48921HelicalSequence AnalysisAdd
    BLAST
    Transmembranei492 – 51221HelicalSequence AnalysisAdd
    BLAST
    Transmembranei627 – 64721HelicalSequence AnalysisAdd
    BLAST
    Transmembranei661 – 68121HelicalSequence AnalysisAdd
    BLAST
    Transmembranei740 – 76021HelicalSequence AnalysisAdd
    BLAST
    Transmembranei778 – 79720HelicalSequence AnalysisAdd
    BLAST
    Transmembranei966 – 98621HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1020 – 104021HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1114 – 113421HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1169 – 118921HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1214 – 123421HelicalSequence AnalysisAdd
    BLAST
    Transmembranei1271 – 129121HelicalSequence AnalysisAdd
    BLAST

    Family & Domainsi

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi288 – 2914Poly-Ala
    Compositional biasi293 – 2964Poly-Asn
    Compositional biasi332 – 34110Asp/Gln/Ser-rich (acidic)
    Compositional biasi369 – 3746Poly-Gln

    Domaini

    The RING-CH-type zinc finger domain is required for E3 ligase activity.

    Sequence similaritiesi

    Belongs to the DOA10/MARCH6 family.Curated
    Contains 1 RING-CH-type zinc finger.PROSITE-ProRule annotation

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri31 – 10070RING-CH-typePROSITE-ProRule annotationAdd
    BLAST

    Keywords - Domaini

    Transmembrane, Transmembrane helix, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG5183.
    GeneTreeiENSGT00730000110355.
    KOiK10661.
    OMAiSHFILGK.
    OrthoDBiEOG7G1VFT.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR011016. Znf_RING-CH.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    PfamiPF12906. RINGv. 1 hit.
    [Graphical view]
    SMARTiSM00744. RINGv. 1 hit.
    [Graphical view]
    PROSITEiPS51292. ZF_RING_CH. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40318-1 [UniParc]FASTAAdd to Basket

    « Hide

    MDVDSDVNVS RLRDELHKVA NEETDTATFN DDAPSGATCR ICRGEATEDN     50
    PLFHPCKCRG SIKYMHESCL LEWVASKNID ISKPGADVKC DICHYPIQFK 100
    TIYAENMPEK IPFSLLLSKS ILTFFEKARL ALTIGLAAVL YIIGVPLVWN 150
    MFGKLYTMML DGSSPYPGDF LKSLIYGYDQ SATPELTTRA IFYQLLQNHS 200
    FTSLQFIMIV ILHIALYFQY DMIVREDVFS KMVFHKIGPR LSPKDLKSRL 250
    KERFPMMDDR MVEYLAREMR AHDENRQEQG HDRLNMPAAA ADNNNNVINP 300
    RNDNVPPQDP NDHRNFENLR HVDELDHDEA TEEHENNDSD NSLPSGDDSS 350
    RILPGSSSDN EEDEEAEGQQ QQQQPEEEAD YRDHIEPNPI DMWANRRAQN 400
    EFDDLIAAQQ NAINRPNAPV FIPPPAQNRA GNVDQDEQDF GAAVGVPPAQ 450
    ANPDDQGQGP LVINLKLKLL NVIAYFIIAV VFTAIYLAIS YLFPTFIGFG 500
    LLKIYFGIFK VILRGLCHLY YLSGAHIAYN GLTKLVPKVD VAMSWISDHL 550
    IHDIIYLYNG YTENTMKHSI FIRALPALTT YLTSVSIVCA SSNLVSRGYG 600
    RENGMSNPTR RLIFQILFAL KCTFKVFTLF FIELAGFPIL AGVMLDFSLF 650
    CPILASNSRM LWVPSICAIW PPFSLFVYWT IGTLYMYWFA KYIGMIRKNI 700
    IRPGVLFFIR SPEDPNIKIL HDSLIHPMSI QLSRLCLSMF IYAIFIVLGF 750
    GFHTRIFFPF MLKSNLLSVP EAYKPTSIIS WKFNTILLTL YFTKRILESS 800
    SYVKPLLERY WKTIFKLCSR KLRLSSFILG KDTPTERGHI VYRNLFYKYI 850
    AAKNAEWSNQ ELFTKPKTLE QAEELFGQVR DVHAYFVPDG VLMRVPSSDI 900
    VSRNYVQTMF VPVTKDDKLL KPLDLERIKE RNKRAAGEFG YLDEQNTEYD 950
    QYYIVYVPPD FRLRYMTLLG LVWLFASILM LGVTFISQAL INFVCSFGFL 1000
    PVVKLLLGER NKVYVAWKEL SDISYSYLNI YYVCVGSVCL SKIAKDILHF 1050
    TEGQNTLDEH AVDENEVEEV EHDIPERDIN NAPVNNINNV EEGQGIFMAI 1100
    FNSIFDSMLV KYNLMVFIAI MIAVIRTMVS WVVLTDGILA CYNYLTIRVF 1150
    GNSSYTIGNS KWFKYDESLL FVVWIISSMV NFGTGYKSLK LFFRNRNTSK 1200
    LNFLKTMALE LFKQGFLHMV IYVLPIIILS LVFLRDVSTK QIIDISHGSR 1250
    SFTLSLNESF PTWTRMQDIY FGLLIALESF TFFFQATVLF IQWFKSTVQN 1300
    VKDEVYTKGR ALENLPDES 1319
    Length:1,319
    Mass (Da):151,455
    Last modified:February 1, 1995 - v1
    Checksum:i3EDFF7F9D90A0C8C
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti241 – 2411L → F in CAA54133. (PubMed:7816042)Curated
    Sequence conflicti743 – 7431A → T in CAA54133. (PubMed:7816042)Curated
    Sequence conflicti1085 – 10851N → D in CAA54133. (PubMed:7816042)Curated
    Sequence conflicti1186 – 11861Y → F in CAA54133. (PubMed:7816042)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76715 Genomic DNA. Translation: CAA54133.1.
    Z46881 Genomic DNA. Translation: CAA86961.1.
    Z46861 Genomic DNA. Translation: CAA86921.1.
    BK006942 Genomic DNA. Translation: DAA08517.1.
    PIRiS49951.
    RefSeqiNP_012234.3. NM_001179380.3.

    Genome annotation databases

    EnsemblFungiiYIL030C; YIL030C; YIL030C.
    GeneIDi854781.
    KEGGisce:YIL030C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76715 Genomic DNA. Translation: CAA54133.1 .
    Z46881 Genomic DNA. Translation: CAA86961.1 .
    Z46861 Genomic DNA. Translation: CAA86921.1 .
    BK006942 Genomic DNA. Translation: DAA08517.1 .
    PIRi S49951.
    RefSeqi NP_012234.3. NM_001179380.3.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2M6M NMR - A 19-101 [» ]
    ProteinModelPortali P40318.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34959. 166 interactions.
    DIPi DIP-7286N.
    IntActi P40318. 81 interactions.
    MINTi MINT-1361830.
    STRINGi 4932.YIL030C.

    Proteomic databases

    MaxQBi P40318.
    PaxDbi P40318.
    PeptideAtlasi P40318.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YIL030C ; YIL030C ; YIL030C .
    GeneIDi 854781.
    KEGGi sce:YIL030C.

    Organism-specific databases

    CYGDi YIL030c.
    SGDi S000001292. SSM4.

    Phylogenomic databases

    eggNOGi COG5183.
    GeneTreei ENSGT00730000110355.
    KOi K10661.
    OMAi SHFILGK.
    OrthoDBi EOG7G1VFT.

    Enzyme and pathway databases

    UniPathwayi UPA00143 .
    BioCyci YEAST:G3O-31303-MONOMER.

    Miscellaneous databases

    NextBioi 977562.
    PROi P40318.

    Gene expression databases

    Genevestigatori P40318.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR011016. Znf_RING-CH.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    Pfami PF12906. RINGv. 1 hit.
    [Graphical view ]
    SMARTi SM00744. RINGv. 1 hit.
    [Graphical view ]
    PROSITEi PS51292. ZF_RING_CH. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Inactivation of SSM4, a new Saccharomyces cerevisiae gene, suppresses mRNA instability due to RNA14 mutations."
      Mandart E., Dufour M.-E., Lacroute F.
      Mol. Gen. Genet. 245:323-333(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 28383 / FL100 / VTT C-80102.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "A conserved ubiquitin ligase of the nuclear envelope/endoplasmic reticulum that functions in both ER-associated and Matalpha2 repressor degradation."
      Swanson R., Locher M., Hochstrasser M.
      Genes Dev. 15:2660-2674(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, SUBCELLULAR LOCATION.
    5. "Ubx2 links the Cdc48 complex to ER-associated protein degradation."
      Neuber O., Jarosch E., Volkwein C., Walter J., Sommer T.
      Nat. Cell Biol. 7:993-998(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH UBX2; UBC6 AND UBC7, IDENTIFICATION IN COMPLEX WITH UBX2 AND CDC48.
    6. "Membrane-bound Ubx2 recruits Cdc48 to ubiquitin ligases and their substrates to ensure efficient ER-associated protein degradation."
      Schuberth C., Buchberger A.
      Nat. Cell Biol. 7:999-1006(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, IDENTIFICATION IN COMPLEX WITH UBX2; CDC48 AND UFD1.
    7. "Distinct ubiquitin-ligase complexes define convergent pathways for the degradation of ER proteins."
      Carvalho P., Goder V., Rapoport T.A.
      Cell 126:361-373(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, IDENTIFICATION IN THE DOA10 COMPLEX WITH CDC48; NPL4; UFD1 AND UBX2.
    8. "Membrane and soluble substrates of the Doa10 ubiquitin ligase are degraded by distinct pathways."
      Ravid T., Kreft S.G., Hochstrasser M.
      EMBO J. 25:533-543(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "Membrane topology of the yeast endoplasmic reticulum-localized ubiquitin ligase Doa10 and comparison with its human ortholog TEB4 (MARCH-VI)."
      Kreft S.G., Wang L., Hochstrasser M.
      J. Biol. Chem. 281:4646-4653(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: TOPOLOGY.
    10. "Spatially regulated ubiquitin ligation by an ER/nuclear membrane ligase."
      Deng M., Hochstrasser M.
      Nature 443:827-831(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, FUNCTION.
    11. "Degradation of a cytosolic protein requires endoplasmic reticulum-associated degradation machinery."
      Metzger M.B., Maurer M.J., Dancy B.M., Michaelis S.
      J. Biol. Chem. 283:32302-32316(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN CYTOSOLIC PROTEIN DEGRADATION.
    12. "Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
      Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
      Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    13. "Ubiquitin chain elongation enzyme Ufd2 regulates a subset of Doa10 substrates."
      Liu C., van Dyk D., Xu P., Choe V., Pan H., Peng J., Andrews B., Rao H.
      J. Biol. Chem. 285:10265-10272(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH PEX29.
    14. "N-terminal acetylation of cellular proteins creates specific degradation signals."
      Hwang C.S., Shemorry A., Varshavsky A.
      Science 327:973-977(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN N-ACETYLATED PROTEIN DEGRADATION.
    15. Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

    Entry informationi

    Entry nameiDOA10_YEAST
    AccessioniPrimary (citable) accession number: P40318
    Secondary accession number(s): D6VVQ1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 130 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
    4. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    5. Yeast chromosome IX
      Yeast (Saccharomyces cerevisiae) chromosome IX: entries and gene names

    External Data

    Dasty 3