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P40034

- JHD1_YEAST

UniProt

P40034 - JHD1_YEAST

Protein

JmjC domain-containing histone demethylation protein 1

Gene

JHD1

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 114 (01 Oct 2014)
      Sequence version 1 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Does not demethylate H3 'Lys-4' nor 'Lys-79'.1 Publication

    Catalytic activityi

    Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.1 Publication
    Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.1 Publication

    Cofactori

    Binds 1 Fe2+ ion per subunit.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei302 – 3021SubstrateBy similarity
    Metal bindingi305 – 3051Iron; catalyticCurated
    Metal bindingi307 – 3071Iron; catalyticPROSITE-ProRule annotation
    Binding sitei322 – 3221SubstrateBy similarity
    Metal bindingi377 – 3771Iron; catalyticPROSITE-ProRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri4 – 7269PHD-type; atypicalAdd
    BLAST

    GO - Molecular functioni

    1. histone demethylase activity (H3-K36 specific) Source: SGD
    2. methylated histone binding Source: SGD
    3. zinc ion binding Source: InterPro

    GO - Biological processi

    1. histone demethylation Source: SGD
    2. histone H3-K36 demethylation Source: GOC
    3. regulation of transcription, DNA-templated Source: UniProtKB-KW
    4. transcription, DNA-templated Source: UniProtKB-KW

    Keywords - Molecular functioni

    Chromatin regulator, Dioxygenase, Oxidoreductase

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    Iron, Metal-binding, Zinc

    Enzyme and pathway databases

    BioCyciYEAST:G3O-30230-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    JmjC domain-containing histone demethylation protein 1 (EC:1.14.11.27)
    Alternative name(s):
    Jumonji/ARID domain-containing protein 1
    ScJHDM1
    [Histone-H3]-lysine-36 demethylase 1
    Gene namesi
    Name:JHD1
    Ordered Locus Names:YER051W
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome V

    Organism-specific databases

    CYGDiYER051w.
    SGDiS000000853. JHD1.

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi305 – 3051H → A: Abolishes histone demethylase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 492492JmjC domain-containing histone demethylation protein 1PRO_0000202630Add
    BLAST

    Proteomic databases

    MaxQBiP40034.
    PaxDbiP40034.
    PRIDEiP40034.

    Expressioni

    Gene expression databases

    GenevestigatoriP40034.

    Interactioni

    Protein-protein interaction databases

    BioGridi36790. 9 interactions.
    DIPiDIP-5335N.
    MINTiMINT-540531.
    STRINGi4932.YER051W.

    Structurei

    3D structure databases

    ProteinModelPortaliP40034.
    SMRiP40034. Positions 21-425.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini254 – 409156JmjCPROSITE-ProRule annotationAdd
    BLAST

    Domaini

    The JmjC domain mediates the demethylation activity.By similarity

    Sequence similaritiesi

    Belongs to the JHDM1 histone demethylase family.Curated
    Contains 1 JmjC domain.PROSITE-ProRule annotation
    Contains 1 PHD-type zinc finger.Curated

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri4 – 7269PHD-type; atypicalAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiNOG290496.
    GeneTreeiENSGT00550000074396.
    HOGENOMiHOG000246712.
    KOiK10276.
    OMAiGTSVYYN.
    OrthoDBiEOG73NGDR.

    Family and domain databases

    Gene3Di3.30.40.10. 1 hit.
    InterProiIPR003347. JmjC_dom.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view]
    SMARTiSM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view]
    SUPFAMiSSF57903. SSF57903. 1 hit.
    PROSITEiPS51184. JMJC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P40034-1 [UniParc]FASTAAdd to Basket

    « Hide

    MQDPNICQHC QLKDNPGALI WVKCDSCPQW VHVKCVPLKR IHYSNLTSSE    50
    VLSYPNSAKQ IKSYRCPNHK EGEYLTAYAL ITQKGKRQRN KENPEDSHIN 100
    KRYNFRKKKL LDYIALNEGE SKRDKMNHPH KESFMKSFEK WKNGSNIINA 150
    ADFAEKFDNI DVPYKIIDPL NSGVYVPNVG TDNGCLTVNY ITEMIGEDYH 200
    VDVMDVQSQM NENWNLGSWN EYFTNTEPDR RDRIRNVISL EVSNIEGLEL 250
    ERPTAVRQND LVDKIWSFNG HLEKVNGEKA EENDPKPKVT KYILMSVKDA 300
    YTDFHLDFAG TSVYYNVISG QKKFLLFPPT QSNIDKYIEW SLKEDQNSVF 350
    LGDILEDGIA MELDAGDLFM IPAGYIHAVY TPVDSLVFGG NFLTIRDLET 400
    HLKIVEIEKL TKVPRRFTFP KFDQVMGKLC EYLALDKNKI TSDVSDGDLL 450
    SRTTNCAIQS LHAYVIKPEV KYKPLNFTSK KHLAKALADL IS 492
    Length:492
    Mass (Da):56,530
    Last modified:February 1, 1995 - v1
    Checksum:i5CBD09352131692B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U18796 Genomic DNA. Translation: AAB64586.1.
    BK006939 Genomic DNA. Translation: DAA07707.1.
    PIRiS50554.
    RefSeqiNP_010971.1. NM_001178942.1.

    Genome annotation databases

    EnsemblFungiiYER051W; YER051W; YER051W.
    GeneIDi856777.
    KEGGisce:YER051W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U18796 Genomic DNA. Translation: AAB64586.1 .
    BK006939 Genomic DNA. Translation: DAA07707.1 .
    PIRi S50554.
    RefSeqi NP_010971.1. NM_001178942.1.

    3D structure databases

    ProteinModelPortali P40034.
    SMRi P40034. Positions 21-425.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 36790. 9 interactions.
    DIPi DIP-5335N.
    MINTi MINT-540531.
    STRINGi 4932.YER051W.

    Proteomic databases

    MaxQBi P40034.
    PaxDbi P40034.
    PRIDEi P40034.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YER051W ; YER051W ; YER051W .
    GeneIDi 856777.
    KEGGi sce:YER051W.

    Organism-specific databases

    CYGDi YER051w.
    SGDi S000000853. JHD1.

    Phylogenomic databases

    eggNOGi NOG290496.
    GeneTreei ENSGT00550000074396.
    HOGENOMi HOG000246712.
    KOi K10276.
    OMAi GTSVYYN.
    OrthoDBi EOG73NGDR.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-30230-MONOMER.

    Miscellaneous databases

    NextBioi 982979.

    Gene expression databases

    Genevestigatori P40034.

    Family and domain databases

    Gene3Di 3.30.40.10. 1 hit.
    InterProi IPR003347. JmjC_dom.
    IPR011011. Znf_FYVE_PHD.
    IPR001965. Znf_PHD.
    IPR013083. Znf_RING/FYVE/PHD.
    [Graphical view ]
    SMARTi SM00558. JmjC. 1 hit.
    SM00249. PHD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF57903. SSF57903. 1 hit.
    PROSITEi PS51184. JMJC. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    2. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    3. Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
    4. "Histone demethylation by a family of JmjC domain-containing proteins."
      Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H., Tempst P., Zhang Y.
      Nature 439:811-816(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, ENZYME ACTIVITY, MUTAGENESIS OF HIS-305.

    Entry informationi

    Entry nameiJHD1_YEAST
    AccessioniPrimary (citable) accession number: P40034
    Secondary accession number(s): D3DLV3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 1, 1995
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 114 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 784 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    3. Yeast chromosome V
      Yeast (Saccharomyces cerevisiae) chromosome V: entries and gene names

    External Data

    Dasty 3