JHD2_YEAST
ID JHD2_YEAST Reviewed; 728 AA.
AC P47156; D6VWT8;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=Histone demethylase JHD2;
DE EC=1.14.11.67 {ECO:0000269|PubMed:17310255};
DE AltName: Full=Jumonji/ARID domain-containing protein 2;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase JHD2 {ECO:0000305};
GN Name=JHD2; OrderedLocusNames=YJR119C; ORFNames=J2035;
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=8641269; DOI=10.1002/j.1460-2075.1996.tb00557.x;
RA Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C.,
RA Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D.,
RA Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J.,
RA Heumann K., Hilger F., Hollenberg C.P., Huang M.-E., Jacq C.,
RA Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E.,
RA Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T.,
RA Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B.,
RA Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R.,
RA Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N.,
RA To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H.,
RA von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X.";
RL EMBO J. 15:2031-2049(1996).
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-427.
RX PubMed=17310255; DOI=10.1038/nsmb1200;
RA Seward D.J., Cubberley G., Kim S., Schonewald M., Zhang L., Tripet B.,
RA Bentley D.L.;
RT "Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC
RT proteins.";
RL Nat. Struct. Mol. Biol. 14:240-242(2007).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3,
CC thereby playing a central role in histone code. Demethylates
CC trimethylated H3 'Lys-4'. {ECO:0000269|PubMed:17310255}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-
CC [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone
CC H3] + 3 succinate; Xref=Rhea:RHEA:60208, Rhea:RHEA-COMP:15537,
CC Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61961; EC=1.14.11.67;
CC Evidence={ECO:0000269|PubMed:17310255};
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:0000255|PROSITE-ProRule:PRU00537}.
CC -!- DOMAIN: The JmjC domain is required for enzymatic activity.
CC -!- MISCELLANEOUS: Present with 290 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; Z49619; CAA89649.1; -; Genomic_DNA.
DR EMBL; Z49620; CAA89651.1; -; Genomic_DNA.
DR EMBL; BK006943; DAA08904.1; -; Genomic_DNA.
DR PIR; S57142; S57142.
DR RefSeq; NP_012653.1; NM_001181777.1.
DR AlphaFoldDB; P47156; -.
DR SMR; P47156; -.
DR BioGRID; 33875; 159.
DR DIP; DIP-4835N; -.
DR IntAct; P47156; 1.
DR MINT; P47156; -.
DR STRING; 4932.YJR119C; -.
DR MaxQB; P47156; -.
DR PaxDb; P47156; -.
DR PRIDE; P47156; -.
DR EnsemblFungi; YJR119C_mRNA; YJR119C; YJR119C.
DR GeneID; 853583; -.
DR KEGG; sce:YJR119C; -.
DR SGD; S000003880; JHD2.
DR VEuPathDB; FungiDB:YJR119C; -.
DR eggNOG; KOG1246; Eukaryota.
DR GeneTree; ENSGT00940000168915; -.
DR HOGENOM; CLU_000991_4_0_1; -.
DR InParanoid; P47156; -.
DR OMA; ANYQHEG; -.
DR BioCyc; YEAST:G3O-31740-MON; -.
DR BRENDA; 1.14.11.67; 984.
DR Reactome; R-SCE-3214842; HDMs demethylate histones.
DR PRO; PR:P47156; -.
DR Proteomes; UP000002311; Chromosome X.
DR RNAct; P47156; protein.
DR GO; GO:0005737; C:cytoplasm; HDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0032453; F:histone H3-methyl-lysine-4 demethylase activity; IDA:SGD.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0071041; P:antisense RNA transcript catabolic process; IMP:SGD.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:1904388; P:negative regulation of ncRNA transcription associated with protein coding gene TSS/TES; IMP:SGD.
DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IMP:SGD.
DR GO; GO:0000183; P:rDNA heterochromatin assembly; IMP:SGD.
DR GO; GO:1902275; P:regulation of chromatin organization; IMP:SGD.
DR GO; GO:0060623; P:regulation of chromosome condensation; IMP:SGD.
DR Gene3D; 3.30.40.10; -; 1.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF00628; PHD; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 1.
DR SUPFAM; SSF57903; SSF57903; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
DR PROSITE; PS01359; ZF_PHD_1; 1.
DR PROSITE; PS50016; ZF_PHD_2; 1.
PE 1: Evidence at protein level;
KW Chromatin regulator; Dioxygenase; Iron; Metal-binding; Nucleus;
KW Oxidoreductase; Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..728
FT /note="Histone demethylase JHD2"
FT /id="PRO_0000203116"
FT DOMAIN 4..47
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 381..549
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 235..285
FT /note="PHD-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT BINDING 427
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000305"
FT BINDING 430
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 517
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT MUTAGEN 427
FT /note="H->A: Abolishes enzymatic activity."
FT /evidence="ECO:0000269|PubMed:17310255"
SQ SEQUENCE 728 AA; 84984 MW; DB22C38B3813F69E CRC64;
MEEIPALYPT EQEFKNPIDY LSNPHIKRLG VRYGMVKVVP PNGFCPPLSI DMENFTFQPR
IQNLENLDLK NRCRLFFMKQ LNNFKRSVKD PSKLILREPY TIVEYSDSTH ASEILKKKVY
FYDVFSELIK DNRTLTDTTQ SFRRKLKFRD ISQLRGDISL WRTISKKFNV PIGLLKEIFE
KYIASYYIFL HSLNENVHTA LHADQYPKSL LSDDEDDFDL GPDSNSGSDF EEDDDDACIV
CRKTNDPKRT ILCDSCDKPF HIYCLSPPLE RVPSGDWICN TCIVGNGYYG FTQDTHDYSL
PEFQEYCKRQ NSRLLPARKL SIDELEEMFW SLVTKNRRSS LTTVKYGADI HNELPGQITG
FPTREFIPKN INGDELIDYL KYCDHPMNLT NLPMAHNSLL PLFKRNISGM TIPWIYIGSL
FSTFCWHMED QYTLSANYQH EGDPKVWYSI PESGCTKFND LLNDMSPDLF IKQPDLLHQL
VTLISPYDPN FKKSGIPVYK AVQKPNEYII TFPKCYHAGF NTGYNFNEAV NFTIDFWLPY
GFGAITDYKL TQKACVFDMF DLMINVLDKY NKDTLLFNDA FVRQCYSSLI VFYNTELKRI
RKIQAIVPRT TLLEVHTDPN DEDEEYDIFC SQCKTICSIA FVLRKNNYDS IRTYKRHKKN
HLSIRQWNEL STTDSKVSIL CTQDYLKSIQ NLNNSDGEEP YIDDELYFTK SLKDIDSLIK
QVGVKLDR
