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P40318

- DOA10_YEAST

UniProt

P40318 - DOA10_YEAST

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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

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. ubiquitin-protein transferase activity Source: SGD
  3. zinc ion binding Source: InterPro

GO - Biological processi

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

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

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 131131CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei132 – 15221HelicalSequence AnalysisAdd
BLAST
Topological domaini153 – 20351LumenalSequence AnalysisAdd
BLAST
Transmembranei204 – 22421HelicalSequence AnalysisAdd
BLAST
Topological domaini225 – 468244CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei469 – 48921HelicalSequence AnalysisAdd
BLAST
Topological domaini490 – 4912LumenalSequence Analysis
Transmembranei492 – 51221HelicalSequence AnalysisAdd
BLAST
Topological domaini513 – 626114CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei627 – 64721HelicalSequence AnalysisAdd
BLAST
Topological domaini648 – 66013LumenalSequence AnalysisAdd
BLAST
Transmembranei661 – 68121HelicalSequence AnalysisAdd
BLAST
Topological domaini682 – 73958CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei740 – 76021HelicalSequence AnalysisAdd
BLAST
Topological domaini761 – 77717LumenalSequence AnalysisAdd
BLAST
Transmembranei778 – 79720HelicalSequence AnalysisAdd
BLAST
Topological domaini798 – 965168CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei966 – 98621HelicalSequence AnalysisAdd
BLAST
Topological domaini987 – 101933LumenalSequence AnalysisAdd
BLAST
Transmembranei1020 – 104021HelicalSequence AnalysisAdd
BLAST
Topological domaini1041 – 111373CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei1114 – 113421HelicalSequence AnalysisAdd
BLAST
Topological domaini1135 – 116834LumenalSequence AnalysisAdd
BLAST
Transmembranei1169 – 118921HelicalSequence AnalysisAdd
BLAST
Topological domaini1190 – 121324CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei1214 – 123421HelicalSequence AnalysisAdd
BLAST
Topological domaini1235 – 127036LumenalSequence AnalysisAdd
BLAST
Transmembranei1271 – 129121HelicalSequence AnalysisAdd
BLAST
Topological domaini1292 – 131928CytoplasmicSequence AnalysisAdd
BLAST

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
Complete GO annotation...

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 – 423Combined sources
Beta strandi48 – 503Combined sources
Helixi67 – 7610Combined sources
Beta strandi91 – 933Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M6MNMR-A19-101[»]
ProteinModelPortaliP40318.
SMRiP40318. Positions 19-101.
ModBaseiSearch...
MobiDBiSearch...

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.
InParanoidiP40318.
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

        10         20         30         40         50
MDVDSDVNVS RLRDELHKVA NEETDTATFN DDAPSGATCR ICRGEATEDN
60 70 80 90 100
PLFHPCKCRG SIKYMHESCL LEWVASKNID ISKPGADVKC DICHYPIQFK
110 120 130 140 150
TIYAENMPEK IPFSLLLSKS ILTFFEKARL ALTIGLAAVL YIIGVPLVWN
160 170 180 190 200
MFGKLYTMML DGSSPYPGDF LKSLIYGYDQ SATPELTTRA IFYQLLQNHS
210 220 230 240 250
FTSLQFIMIV ILHIALYFQY DMIVREDVFS KMVFHKIGPR LSPKDLKSRL
260 270 280 290 300
KERFPMMDDR MVEYLAREMR AHDENRQEQG HDRLNMPAAA ADNNNNVINP
310 320 330 340 350
RNDNVPPQDP NDHRNFENLR HVDELDHDEA TEEHENNDSD NSLPSGDDSS
360 370 380 390 400
RILPGSSSDN EEDEEAEGQQ QQQQPEEEAD YRDHIEPNPI DMWANRRAQN
410 420 430 440 450
EFDDLIAAQQ NAINRPNAPV FIPPPAQNRA GNVDQDEQDF GAAVGVPPAQ
460 470 480 490 500
ANPDDQGQGP LVINLKLKLL NVIAYFIIAV VFTAIYLAIS YLFPTFIGFG
510 520 530 540 550
LLKIYFGIFK VILRGLCHLY YLSGAHIAYN GLTKLVPKVD VAMSWISDHL
560 570 580 590 600
IHDIIYLYNG YTENTMKHSI FIRALPALTT YLTSVSIVCA SSNLVSRGYG
610 620 630 640 650
RENGMSNPTR RLIFQILFAL KCTFKVFTLF FIELAGFPIL AGVMLDFSLF
660 670 680 690 700
CPILASNSRM LWVPSICAIW PPFSLFVYWT IGTLYMYWFA KYIGMIRKNI
710 720 730 740 750
IRPGVLFFIR SPEDPNIKIL HDSLIHPMSI QLSRLCLSMF IYAIFIVLGF
760 770 780 790 800
GFHTRIFFPF MLKSNLLSVP EAYKPTSIIS WKFNTILLTL YFTKRILESS
810 820 830 840 850
SYVKPLLERY WKTIFKLCSR KLRLSSFILG KDTPTERGHI VYRNLFYKYI
860 870 880 890 900
AAKNAEWSNQ ELFTKPKTLE QAEELFGQVR DVHAYFVPDG VLMRVPSSDI
910 920 930 940 950
VSRNYVQTMF VPVTKDDKLL KPLDLERIKE RNKRAAGEFG YLDEQNTEYD
960 970 980 990 1000
QYYIVYVPPD FRLRYMTLLG LVWLFASILM LGVTFISQAL INFVCSFGFL
1010 1020 1030 1040 1050
PVVKLLLGER NKVYVAWKEL SDISYSYLNI YYVCVGSVCL SKIAKDILHF
1060 1070 1080 1090 1100
TEGQNTLDEH AVDENEVEEV EHDIPERDIN NAPVNNINNV EEGQGIFMAI
1110 1120 1130 1140 1150
FNSIFDSMLV KYNLMVFIAI MIAVIRTMVS WVVLTDGILA CYNYLTIRVF
1160 1170 1180 1190 1200
GNSSYTIGNS KWFKYDESLL FVVWIISSMV NFGTGYKSLK LFFRNRNTSK
1210 1220 1230 1240 1250
LNFLKTMALE LFKQGFLHMV IYVLPIIILS LVFLRDVSTK QIIDISHGSR
1260 1270 1280 1290 1300
SFTLSLNESF PTWTRMQDIY FGLLIALESF TFFFQATVLF IQWFKSTVQN
1310
VKDEVYTKGR ALENLPDES
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2M6M NMR - A 19-101 [» ]
ProteinModelPortali P40318.
SMRi P40318. Positions 19-101.
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.
InParanoidi P40318.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 132 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