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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

Miscellaneous

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

Catalytic activityi

Protein N6,N6-dimethyl-L-lysine + 2 2-oxoglutarate + 2 O2 = protein L-lysine + 2 succinate + 2 formaldehyde + 2 CO2.1 Publication

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei302SubstrateBy similarity1
Metal bindingi305Iron; catalyticCurated1
Metal bindingi307Iron; catalyticPROSITE-ProRule annotation1
Binding sitei322SubstrateBy similarity1
Metal bindingi377Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri4 – 72PHD-type; atypicalAdd BLAST69

GO - Molecular functioni

  • histone demethylase activity (H3-K36 specific) Source: SGD
  • metal ion binding Source: UniProtKB-KW
  • methylated histone binding Source: SGD

GO - Biological processi

  • histone demethylation Source: SGD
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • transcription, DNA-templated Source: UniProtKB-KW

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase
Biological processTranscription, Transcription regulation
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciYEAST:G3O-30230-MONOMER.
BRENDAi1.14.11.27. 984.
ReactomeiR-SCE-2299718. Condensation of Prophase Chromosomes.
R-SCE-3214842. HDMs demethylate histones.
R-SCE-8951664. Neddylation.
R-SCE-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
JmjC domain-containing histone demethylation protein 1 (EC:1.14.11.271 Publication)
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
Proteomesi
  • UP000002311 Componenti: Chromosome V

Organism-specific databases

EuPathDBiFungiDB:YER051W.
SGDiS000000853. JHD1.

Subcellular locationi

GO - Cellular componenti

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi305H → A: Abolishes histone demethylase activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002026301 – 492JmjC domain-containing histone demethylation protein 1Add BLAST492

Proteomic databases

MaxQBiP40034.
PRIDEiP40034.

Interactioni

GO - Molecular functioni

  • methylated histone binding Source: SGD

Protein-protein interaction databases

BioGridi36790. 31 interactors.
DIPiDIP-5335N.
MINTiMINT-540531.
STRINGi4932.YER051W.

Structurei

3D structure databases

ProteinModelPortaliP40034.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini254 – 409JmjCPROSITE-ProRule annotationAdd BLAST156

Domaini

The JmjC domain mediates the demethylation activity.By similarity

Sequence similaritiesi

Belongs to the JHDM1 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri4 – 72PHD-type; atypicalAdd BLAST69

Keywords - Domaini

Zinc-finger

Phylogenomic databases

GeneTreeiENSGT00550000074396.
HOGENOMiHOG000246712.
InParanoidiP40034.
KOiK10276.
OMAiFRFPMFN.
OrthoDBiEOG092C3QJU.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiView protein in InterPro
IPR003347. JmjC_dom.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
SMARTiView protein in SMART
SM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiView protein in PROSITE
PS51184. JMJC. 1 hit.

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.

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.

Entry informationi

Entry nameiJHD1_YEAST
AccessioniPrimary (citable) accession number: P40034
Secondary accession number(s): D3DLV3
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: February 1, 1995
Last modified: July 5, 2017
This is version 137 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

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