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Protein

Histone demethylase JHD2

Gene

JHD2

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated H3 'Lys-4'.1 Publication

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi427 – 4271Iron; catalyticCurated
Metal bindingi430 – 4301Iron; catalyticPROSITE-ProRule annotation
Metal bindingi517 – 5171Iron; catalyticPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 28551PHD-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  • dioxygenase activity Source: UniProtKB-KW
  • histone demethylase activity (H3-K4 specific) Source: SGD
  • histone demethylase activity (H3-monomethyl-K4 specific) Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • antisense RNA transcript catabolic process Source: SGD
  • chromatin silencing at rDNA Source: SGD
  • histone demethylation Source: SGD
  • histone H3-K4 demethylation Source: SGD
  • negative regulation of ncRNA transcription associated with protein coding gene TSS/TES Source: SGD
  • positive regulation of transcription from RNA polymerase II promoter Source: SGD
  • regulation of chromosome condensation Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-31740-MONOMER.
ReactomeiR-SCE-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Histone demethylase JHD2 (EC:1.14.11.-)
Alternative name(s):
Jumonji/ARID domain-containing protein 2
Gene namesi
Name:JHD2
Ordered Locus Names:YJR119C
ORF Names:J2035
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome X

Organism-specific databases

EuPathDBiFungiDB:YJR119C.
SGDiS000003880. JHD2.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi427 – 4271H → A: Abolishes enzymatic activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 728728Histone demethylase JHD2PRO_0000203116Add
BLAST

Proteomic databases

MaxQBiP47156.

Interactioni

Protein-protein interaction databases

BioGridi33875. 67 interactions.
DIPiDIP-4835N.
IntActiP47156. 1 interaction.
MINTiMINT-537060.

Structurei

3D structure databases

ProteinModelPortaliP47156.
SMRiP47156. Positions 1-103, 234-567.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini4 – 4744JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini381 – 549169JmjCPROSITE-ProRule annotationAdd
BLAST

Domaini

The JmjC domain is required for enzymatic activity.

Sequence similaritiesi

Belongs to the JARID1 histone demethylase family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri235 – 28551PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00530000063118.
HOGENOMiHOG000113131.
InParanoidiP47156.
KOiK11446.
OMAiISESICC.
OrthoDBiEOG7SXWBR.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P47156-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEEIPALYPT EQEFKNPIDY LSNPHIKRLG VRYGMVKVVP PNGFCPPLSI
60 70 80 90 100
DMENFTFQPR IQNLENLDLK NRCRLFFMKQ LNNFKRSVKD PSKLILREPY
110 120 130 140 150
TIVEYSDSTH ASEILKKKVY FYDVFSELIK DNRTLTDTTQ SFRRKLKFRD
160 170 180 190 200
ISQLRGDISL WRTISKKFNV PIGLLKEIFE KYIASYYIFL HSLNENVHTA
210 220 230 240 250
LHADQYPKSL LSDDEDDFDL GPDSNSGSDF EEDDDDACIV CRKTNDPKRT
260 270 280 290 300
ILCDSCDKPF HIYCLSPPLE RVPSGDWICN TCIVGNGYYG FTQDTHDYSL
310 320 330 340 350
PEFQEYCKRQ NSRLLPARKL SIDELEEMFW SLVTKNRRSS LTTVKYGADI
360 370 380 390 400
HNELPGQITG FPTREFIPKN INGDELIDYL KYCDHPMNLT NLPMAHNSLL
410 420 430 440 450
PLFKRNISGM TIPWIYIGSL FSTFCWHMED QYTLSANYQH EGDPKVWYSI
460 470 480 490 500
PESGCTKFND LLNDMSPDLF IKQPDLLHQL VTLISPYDPN FKKSGIPVYK
510 520 530 540 550
AVQKPNEYII TFPKCYHAGF NTGYNFNEAV NFTIDFWLPY GFGAITDYKL
560 570 580 590 600
TQKACVFDMF DLMINVLDKY NKDTLLFNDA FVRQCYSSLI VFYNTELKRI
610 620 630 640 650
RKIQAIVPRT TLLEVHTDPN DEDEEYDIFC SQCKTICSIA FVLRKNNYDS
660 670 680 690 700
IRTYKRHKKN HLSIRQWNEL STTDSKVSIL CTQDYLKSIQ NLNNSDGEEP
710 720
YIDDELYFTK SLKDIDSLIK QVGVKLDR
Length:728
Mass (Da):84,984
Last modified:February 1, 1996 - v1
Checksum:iDB22C38B3813F69E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49619 Genomic DNA. Translation: CAA89649.1.
Z49620 Genomic DNA. Translation: CAA89651.1.
BK006943 Genomic DNA. Translation: DAA08904.1.
PIRiS57142.
RefSeqiNP_012653.1. NM_001181777.1.

Genome annotation databases

EnsemblFungiiYJR119C; YJR119C; YJR119C.
GeneIDi853583.
KEGGisce:YJR119C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Z49619 Genomic DNA. Translation: CAA89649.1.
Z49620 Genomic DNA. Translation: CAA89651.1.
BK006943 Genomic DNA. Translation: DAA08904.1.
PIRiS57142.
RefSeqiNP_012653.1. NM_001181777.1.

3D structure databases

ProteinModelPortaliP47156.
SMRiP47156. Positions 1-103, 234-567.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi33875. 67 interactions.
DIPiDIP-4835N.
IntActiP47156. 1 interaction.
MINTiMINT-537060.

Proteomic databases

MaxQBiP47156.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYJR119C; YJR119C; YJR119C.
GeneIDi853583.
KEGGisce:YJR119C.

Organism-specific databases

EuPathDBiFungiDB:YJR119C.
SGDiS000003880. JHD2.

Phylogenomic databases

GeneTreeiENSGT00530000063118.
HOGENOMiHOG000113131.
InParanoidiP47156.
KOiK11446.
OMAiISESICC.
OrthoDBiEOG7SXWBR.

Enzyme and pathway databases

BioCyciYEAST:G3O-31740-MONOMER.
ReactomeiR-SCE-3214842. HDMs demethylate histones.

Miscellaneous databases

PROiP47156.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X."
    Galibert F., Alexandraki D., Baur A., Boles E., Chalwatzis N., Chuat J.-C., Coster F., Cziepluch C., de Haan M., Domdey H., Durand P., Entian K.-D., Gatius M., Goffeau A., Grivell L.A., Hennemann A., Herbert C.J., Heumann K.
    , Hilger F., Hollenberg C.P., Huang M.-E., Jacq C., Jauniaux J.-C., Katsoulou C., Kirchrath L., Kleine K., Kordes E., Koetter P., Liebl S., Louis E.J., Manus V., Mewes H.-W., Miosga T., Obermaier B., Perea J., Pohl T.M., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rasmussen S.W., Rose M., Rossau R., Schaaff-Gerstenschlaeger I., Smits P.H.M., Scarcez T., Soriano N., To Van D., Tzermia M., Van Broekhoven A., Vandenbol M., Wedler H., von Wettstein D., Wambutt R., Zagulski M., Zollner A., Karpfinger-Hartl L.
    EMBO J. 15:2031-2049(1996) [PubMed] [Europe PMC] [Abstract]
    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. "Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins."
    Seward D.J., Cubberley G., Kim S., Schonewald M., Zhang L., Tripet B., Bentley D.L.
    Nat. Struct. Mol. Biol. 14:240-242(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF HIS-427.

Entry informationi

Entry nameiJHD2_YEAST
AccessioniPrimary (citable) accession number: P47156
Secondary accession number(s): D6VWT8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 1, 1996
Last sequence update: February 1, 1996
Last modified: June 8, 2016
This is version 134 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 290 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 X
    Yeast (Saccharomyces cerevisiae) chromosome X: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.