JHD1_YEAST
ID JHD1_YEAST Reviewed; 492 AA.
AC P40034; D3DLV3;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1995, sequence version 1.
DT 03-AUG-2022, entry version 165.
DE RecName: Full=JmjC domain-containing histone demethylation protein 1;
DE EC=1.14.11.27 {ECO:0000269|PubMed:16362057};
DE AltName: Full=Jumonji/ARID domain-containing protein 1;
DE AltName: Full=ScJHDM1;
DE AltName: Full=[Histone-H3]-lysine-36 demethylase 1;
GN Name=JHD1; OrderedLocusNames=YER051W;
OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX NCBI_TaxID=559292;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169868;
RA Dietrich F.S., Mulligan J.T., Hennessy K.M., Yelton M.A., Allen E.,
RA Araujo R., Aviles E., Berno A., Brennan T., Carpenter J., Chen E.,
RA Cherry J.M., Chung E., Duncan M., Guzman E., Hartzell G., Hunicke-Smith S.,
RA Hyman R.W., Kayser A., Komp C., Lashkari D., Lew H., Lin D., Mosedale D.,
RA Nakahara K., Namath A., Norgren R., Oefner P., Oh C., Petel F.X.,
RA Roberts D., Sehl P., Schramm S., Shogren T., Smith V., Taylor P., Wei Y.,
RA Botstein D., Davis R.W.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome V.";
RL Nature 387:78-81(1997).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=24374639; DOI=10.1534/g3.113.008995;
RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL G3 (Bethesda) 4:389-398(2014).
RN [3]
RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX PubMed=14562106; DOI=10.1038/nature02046;
RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA O'Shea E.K., Weissman J.S.;
RT "Global analysis of protein expression in yeast.";
RL Nature 425:737-741(2003).
RN [4]
RP FUNCTION, CATALYTIC ACTIVITY, AND MUTAGENESIS OF HIS-305.
RX PubMed=16362057; DOI=10.1038/nature04433;
RA Tsukada Y., Fang J., Erdjument-Bromage H., Warren M.E., Borchers C.H.,
RA Tempst P., Zhang Y.;
RT "Histone demethylation by a family of JmjC domain-containing proteins.";
RL Nature 439:811-816(2006).
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-36'
CC of histone H3, thereby playing a central role in histone code. Does not
CC demethylate H3 'Lys-4' nor 'Lys-79'. {ECO:0000269|PubMed:16362057}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(36)-[histone H3]
CC + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl(36)-[histone H3] + 2
CC succinate; Xref=Rhea:RHEA:42032, Rhea:RHEA-COMP:9785, Rhea:RHEA-
CC COMP:9787, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:61976; EC=1.14.11.27;
CC Evidence={ECO:0000269|PubMed:16362057};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- DOMAIN: The JmjC domain mediates the demethylation activity.
CC {ECO:0000250}.
CC -!- MISCELLANEOUS: Present with 784 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the JHDM1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; U18796; AAB64586.1; -; Genomic_DNA.
DR EMBL; BK006939; DAA07707.1; -; Genomic_DNA.
DR PIR; S50554; S50554.
DR RefSeq; NP_010971.1; NM_001178942.1.
DR AlphaFoldDB; P40034; -.
DR SMR; P40034; -.
DR BioGRID; 36790; 35.
DR DIP; DIP-5335N; -.
DR STRING; 4932.YER051W; -.
DR MaxQB; P40034; -.
DR PaxDb; P40034; -.
DR PRIDE; P40034; -.
DR EnsemblFungi; YER051W_mRNA; YER051W; YER051W.
DR GeneID; 856777; -.
DR KEGG; sce:YER051W; -.
DR SGD; S000000853; JHD1.
DR VEuPathDB; FungiDB:YER051W; -.
DR eggNOG; KOG1633; Eukaryota.
DR GeneTree; ENSGT01040000244400; -.
DR HOGENOM; CLU_003540_6_2_1; -.
DR InParanoid; P40034; -.
DR OMA; MSVGNAY; -.
DR BioCyc; YEAST:G3O-30230-MON; -.
DR BRENDA; 1.14.11.27; 984.
DR PRO; PR:P40034; -.
DR Proteomes; UP000002311; Chromosome V.
DR RNAct; P40034; protein.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0140680; F:histone H3-di/monomethyl-lysine-36 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0051864; F:histone H3-methyl-lysine-36 demethylase activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0035064; F:methylated histone binding; IDA:SGD.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IGI:SGD.
DR GO; GO:0006482; P:protein demethylation; IBA:GO_Central.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Reference proteome; Transcription;
KW Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..492
FT /note="JmjC domain-containing histone demethylation protein
FT 1"
FT /id="PRO_0000202630"
FT DOMAIN 254..409
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 4..72
FT /note="PHD-type; atypical"
FT BINDING 302
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 305
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305"
FT BINDING 307
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 322
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 377
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT MUTAGEN 305
FT /note="H->A: Abolishes histone demethylase activity."
FT /evidence="ECO:0000269|PubMed:16362057"
SQ SEQUENCE 492 AA; 56530 MW; 5CBD09352131692B CRC64;
MQDPNICQHC QLKDNPGALI WVKCDSCPQW VHVKCVPLKR IHYSNLTSSE VLSYPNSAKQ
IKSYRCPNHK EGEYLTAYAL ITQKGKRQRN KENPEDSHIN KRYNFRKKKL LDYIALNEGE
SKRDKMNHPH KESFMKSFEK WKNGSNIINA ADFAEKFDNI DVPYKIIDPL NSGVYVPNVG
TDNGCLTVNY ITEMIGEDYH VDVMDVQSQM NENWNLGSWN EYFTNTEPDR RDRIRNVISL
EVSNIEGLEL ERPTAVRQND LVDKIWSFNG HLEKVNGEKA EENDPKPKVT KYILMSVKDA
YTDFHLDFAG TSVYYNVISG QKKFLLFPPT QSNIDKYIEW SLKEDQNSVF LGDILEDGIA
MELDAGDLFM IPAGYIHAVY TPVDSLVFGG NFLTIRDLET HLKIVEIEKL TKVPRRFTFP
KFDQVMGKLC EYLALDKNKI TSDVSDGDLL SRTTNCAIQS LHAYVIKPEV KYKPLNFTSK
KHLAKALADL IS
