Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

JmjC domain-containing histone demethylation protein 1

Gene

JHD1

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 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

Fe2+By similarityNote: 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

  • histone demethylase activity (H3-K36 specific) Source: SGD
  • methylated histone binding Source: SGD
  • zinc ion binding Source: InterPro

GO - Biological processi

  • histone demethylation Source: SGD
  • histone H3-K36 demethylation Source: GOC
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

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.
BRENDAi1.14.11.27. 984.

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 Componenti: Chromosome V

Organism-specific databases

CYGDiYER051w.
EuPathDBiFungiDB:YER051W.
SGDiS000000853. JHD1.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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.

Interactioni

Protein-protein interaction databases

BioGridi36790. 10 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.
InParanoidiP40034.
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

        10         20         30         40         50
MQDPNICQHC QLKDNPGALI WVKCDSCPQW VHVKCVPLKR IHYSNLTSSE
60 70 80 90 100
VLSYPNSAKQ IKSYRCPNHK EGEYLTAYAL ITQKGKRQRN KENPEDSHIN
110 120 130 140 150
KRYNFRKKKL LDYIALNEGE SKRDKMNHPH KESFMKSFEK WKNGSNIINA
160 170 180 190 200
ADFAEKFDNI DVPYKIIDPL NSGVYVPNVG TDNGCLTVNY ITEMIGEDYH
210 220 230 240 250
VDVMDVQSQM NENWNLGSWN EYFTNTEPDR RDRIRNVISL EVSNIEGLEL
260 270 280 290 300
ERPTAVRQND LVDKIWSFNG HLEKVNGEKA EENDPKPKVT KYILMSVKDA
310 320 330 340 350
YTDFHLDFAG TSVYYNVISG QKKFLLFPPT QSNIDKYIEW SLKEDQNSVF
360 370 380 390 400
LGDILEDGIA MELDAGDLFM IPAGYIHAVY TPVDSLVFGG NFLTIRDLET
410 420 430 440 450
HLKIVEIEKL TKVPRRFTFP KFDQVMGKLC EYLALDKNKI TSDVSDGDLL
460 470 480 490
SRTTNCAIQS LHAYVIKPEV KYKPLNFTSK KHLAKALADL IS
Length:492
Mass (Da):56,530
Last modified:February 1, 1995 - v1
Checksum:i5CBD09352131692B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
Links Updated
U18796 Genomic DNA. Translation: AAB64586.1.
BK006939 Genomic DNA. Translation: DAA07707.1.
PIRiS50554.
RefSeqiNP_010971.1. NM_001178942.1.

3D structure databases

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

Protein-protein interaction databases

BioGridi36790. 10 interactions.
DIPiDIP-5335N.
MINTiMINT-540531.
STRINGi4932.YER051W.

Proteomic databases

MaxQBiP40034.
PaxDbiP40034.
PRIDEiP40034.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CYGDiYER051w.
EuPathDBiFungiDB:YER051W.
SGDiS000000853. JHD1.

Phylogenomic databases

eggNOGiNOG290496.
GeneTreeiENSGT00550000074396.
HOGENOMiHOG000246712.
InParanoidiP40034.
KOiK10276.
OMAiGTSVYYN.
OrthoDBiEOG73NGDR.

Enzyme and pathway databases

BioCyciYEAST:G3O-30230-MONOMER.
BRENDAi1.14.11.27. 984.

Miscellaneous databases

NextBioi982979.
PROiP40034.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: June 24, 2015
This is version 121 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

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 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.