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Protein

JmjC domain-containing histone demethylation protein 1

Gene

Kdm2

Organism
Drosophila melanogaster (Fruit fly)
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.By similarity

Catalytic activityi

Protein N6,N(6)-dimethyl-L-lysine + 2-oxoglutarate + O2 = protein N(6)-methyl-L-lysine + succinate + formaldehyde + CO2.
Protein N(6)-methyl-L-lysine + 2-oxoglutarate + O2 = protein L-lysine + succinate + formaldehyde + CO2.

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei241SubstrateBy similarity1
Metal bindingi244Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi246Iron; catalyticPROSITE-ProRule annotation1
Binding sitei261SubstrateBy similarity1
Metal bindingi316Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri671 – 717CXXC-typePROSITE-ProRule annotationAdd BLAST47

GO - Molecular functioni

GO - Biological processi

  • histone H2A ubiquitination Source: FlyBase
  • histone H3-K36 demethylation Source: FlyBase
  • histone H3-K4 demethylation, trimethyl-H3-K4-specific Source: FlyBase
  • larval somatic muscle development Source: FlyBase
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • SCF-dependent proteasomal ubiquitin-dependent protein catabolic process Source: FlyBase
  • segment specification Source: FlyBase
  • sensory perception of pain Source: FlyBase
  • 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

BRENDAi1.14.11.27. 1994.
ReactomeiR-DME-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Names & Taxonomyi

Protein namesi
Recommended name:
JmjC domain-containing histone demethylation protein 1 (EC:1.14.11.27)
Alternative name(s):
Lysine (K)-specific demethylase 2
[Histone-H3]-lysine-36 demethylase 1
Gene namesi
Name:Kdm2
Synonyms:Jhd1
ORF Names:CG11033
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 3R

Organism-specific databases

FlyBaseiFBgn0037659. Kdm2.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: FlyBase
  • PcG protein complex Source: FlyBase
  • SCF ubiquitin ligase complex Source: FlyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002267901 – 1345JmjC domain-containing histone demethylation protein 1Add BLAST1345

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei53Phosphotyrosine1 Publication1
Modified residuei58Phosphoserine1 Publication1
Modified residuei79Phosphoserine1 Publication1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ9VHH9.
PRIDEiQ9VHH9.

PTM databases

iPTMnetiQ9VHH9.

Expressioni

Gene expression databases

BgeeiFBgn0037659.
ExpressionAtlasiQ9VHH9. baseline.
GenevisibleiQ9VHH9. DM.

Interactioni

Protein-protein interaction databases

BioGridi66257. 1 interactor.
IntActiQ9VHH9. 1 interactor.
MINTiMINT-964793.
STRINGi7227.FBpp0289915.

Structurei

3D structure databases

ProteinModelPortaliQ9VHH9.
SMRiQ9VHH9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini180 – 348JmjCPROSITE-ProRule annotationAdd BLAST169
Domaini1059 – 1105F-boxAdd BLAST47

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi592 – 669Gly-richAdd BLAST78

Domaini

The JmjC domain mediates the demethylation activity.By similarity

Sequence similaritiesi

Belongs to the JHDM1 histone demethylase family.Curated
Contains 1 CXXC-type zinc finger.PROSITE-ProRule annotation
Contains 1 F-box domain.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri671 – 717CXXC-typePROSITE-ProRule annotationAdd BLAST47

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
KOG1947. Eukaryota.
ENOG410XQXU. LUCA.
GeneTreeiENSGT00550000074396.
InParanoidiQ9VHH9.
KOiK10276.
OMAiEEACDQQ.
OrthoDBiEOG091G02DL.
PhylomeDBiQ9VHH9.

Family and domain databases

Gene3Di3.80.10.10. 1 hit.
InterProiIPR001810. F-box_dom.
IPR003347. JmjC_dom.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR006553. Leu-rich_rpt_Cys-con_subtyp.
IPR002857. Znf_CXXC.
IPR019787. Znf_PHD-finger.
[Graphical view]
PfamiPF12937. F-box-like. 1 hit.
PF13516. LRR_6. 1 hit.
PF16866. PHD_4. 1 hit.
PF02008. zf-CXXC. 1 hit.
[Graphical view]
SMARTiSM00256. FBOX. 1 hit.
SM00558. JmjC. 1 hit.
SM00367. LRR_CC. 5 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51058. ZF_CXXC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9VHH9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTAVETGSS PAKSNSNNSS SGGNNNNGNG NLSPNAKGVQ RRQLRERKQR
60 70 80 90 100
KLYLEEWSLG DEDGEGTRGF SVAEKLESSK FAQAGMVREM RGCDLTVAFL
110 120 130 140 150
QQHGFNIPLL FRDKAGLGLR MPDPQEFTVN DVRLCVGSRR LLDVMDVNTQ
160 170 180 190 200
KNLQMTMKEW QQYYDSPQKD RLLNVISLEF SHTRLDRFVQ SPEIVRQIDW
210 220 230 240 250
VDVVWPKQLK DAQREGTNLL GGMMYPKVQK YCLMSVKNCY TDFHIDFGGT
260 270 280 290 300
SVWYHILRGS KVFWLIPPTD RNLQLYEKWV LSGKQADIFF GDTVEKCARV
310 320 330 340 350
YLTAGNTFFI PTGWIHAVYT PTQSLVFGGN FLHSFGIVKQ LKTASVEDST
360 370 380 390 400
KVPQKFRYPF FTEMLWYVLA RYVHTLLGHS HLEGEASLSE DEMAARPHTH
410 420 430 440 450
LTHHELFGLK EIVMYLYDLP PQKKNVPSLV LDPVALIKDV RSLVERHCKD
460 470 480 490 500
QQDLAITGVS VLKSPPGSQP PFLLYDRTRV KQEIKQEIAR KNAEVIREQQ
510 520 530 540 550
QLEAGRAREA ESDTSQSTGV GSVIGMGAGV EYSNGVMKKE QLENGSGVTV
560 570 580 590 600
GGHGSQPEAT FALPTDTLKY RPPKKMHLAT ALVAAAASSS SGGGGPVAGV
610 620 630 640 650
GGSAVVGSSH SPTGGGVGPV TGAGGAISVI ATSSSYIEGG QVGGILNMDN
660 670 680 690 700
CHSPEGGGAK LSPNLTGTGQ PRRRRTRCKN CAACQRSDCG TCPFCMDMVK
710 720 730 740 750
FGGPGRAKQT CMMRQCLSPM LPVTAQCVYC HLDGWRQTPV SPQTKQLASA
760 770 780 790 800
DGPSALMECS VCYEIAHPDC ALSQLDGTED AADAKGIVNE DLPNSWECPS
810 820 830 840 850
CCRSGKNYDY KPRHFRARQK SSEVRRVSVS HGQGGAEGHA DGNTLLPPPV
860 870 880 890 900
GQYNDFVFTS ESEMESGTVS GHMTHWKHGM KRHHQLEVKT ERNNSCDTPS
910 920 930 940 950
PGISPNAIGG DSKVGKRRKS DDGTSVSSSM HESNDAPCGS SAEGAGGAGN
960 970 980 990 1000
ANVSTNQWSG SGGGGGSRKK NSIRSQLAQQ MLNSSTRVLK KPQYVVRPAS
1010 1020 1030 1040 1050
GTGSSSSSGN GGSASATNGI SNGSNQSGAN SCGAGNGERG TNNGGLSGSN
1060 1070 1080 1090 1100
GLGNQHYSSS QNLALDPTVL KIIFRYLPQD TLVTCCSVCK VWSNAAVDPD
1110 1120 1130 1140 1150
LWKKMNCSEH KMSASLLTAI VRRQPEHLIL DWTQIAKRQL AWLVARLPAL
1160 1170 1180 1190 1200
KNLSLQNCPI QAVLALHTCL CPPLQTLDLS FVRGLNDAAI RDILSPPKDS
1210 1220 1230 1240 1250
RPGLSDSKTR LRDLKVMKLA GTDISDVAVR YITQSLPYLR HLDLSSCQRI
1260 1270 1280 1290 1300
TDAGVAQIGT STTATARLTE LNLSACRLVS ENALEHLAKC EGLIWLDLRH
1310 1320 1330 1340
VPQVSTQSVI RFASNSKHDL CVRDIKLVER RRRNSTTANR SWHHD
Length:1,345
Mass (Da):146,178
Last modified:March 7, 2006 - v2
Checksum:i3157AD3B9E1AE619
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti469Q → L in AAQ22410 (Ref. 3) Curated1
Sequence conflicti950N → T in AAQ22410 (Ref. 3) Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014297 Genomic DNA. Translation: AAF54335.2.
BT009941 mRNA. Translation: AAQ22410.1.
RefSeqiNP_001262400.1. NM_001275471.1.
NP_001262401.1. NM_001275472.1.
NP_001262402.1. NM_001275473.1.
NP_649864.2. NM_141607.3.
UniGeneiDm.18939.

Genome annotation databases

EnsemblMetazoaiFBtr0300691; FBpp0289915; FBgn0037659.
FBtr0336758; FBpp0307734; FBgn0037659.
FBtr0336759; FBpp0307735; FBgn0037659.
FBtr0336760; FBpp0307736; FBgn0037659.
GeneIDi41090.
KEGGidme:Dmel_CG11033.
UCSCiCG11033-RA. d. melanogaster.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE014297 Genomic DNA. Translation: AAF54335.2.
BT009941 mRNA. Translation: AAQ22410.1.
RefSeqiNP_001262400.1. NM_001275471.1.
NP_001262401.1. NM_001275472.1.
NP_001262402.1. NM_001275473.1.
NP_649864.2. NM_141607.3.
UniGeneiDm.18939.

3D structure databases

ProteinModelPortaliQ9VHH9.
SMRiQ9VHH9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi66257. 1 interactor.
IntActiQ9VHH9. 1 interactor.
MINTiMINT-964793.
STRINGi7227.FBpp0289915.

PTM databases

iPTMnetiQ9VHH9.

Proteomic databases

PaxDbiQ9VHH9.
PRIDEiQ9VHH9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0300691; FBpp0289915; FBgn0037659.
FBtr0336758; FBpp0307734; FBgn0037659.
FBtr0336759; FBpp0307735; FBgn0037659.
FBtr0336760; FBpp0307736; FBgn0037659.
GeneIDi41090.
KEGGidme:Dmel_CG11033.
UCSCiCG11033-RA. d. melanogaster.

Organism-specific databases

CTDi41090.
FlyBaseiFBgn0037659. Kdm2.

Phylogenomic databases

eggNOGiKOG1633. Eukaryota.
KOG1947. Eukaryota.
ENOG410XQXU. LUCA.
GeneTreeiENSGT00550000074396.
InParanoidiQ9VHH9.
KOiK10276.
OMAiEEACDQQ.
OrthoDBiEOG091G02DL.
PhylomeDBiQ9VHH9.

Enzyme and pathway databases

BRENDAi1.14.11.27. 1994.
ReactomeiR-DME-983168. Antigen processing: Ubiquitination & Proteasome degradation.

Miscellaneous databases

GenomeRNAii41090.
PROiQ9VHH9.

Gene expression databases

BgeeiFBgn0037659.
ExpressionAtlasiQ9VHH9. baseline.
GenevisibleiQ9VHH9. DM.

Family and domain databases

Gene3Di3.80.10.10. 1 hit.
InterProiIPR001810. F-box_dom.
IPR003347. JmjC_dom.
IPR032675. L_dom-like.
IPR001611. Leu-rich_rpt.
IPR006553. Leu-rich_rpt_Cys-con_subtyp.
IPR002857. Znf_CXXC.
IPR019787. Znf_PHD-finger.
[Graphical view]
PfamiPF12937. F-box-like. 1 hit.
PF13516. LRR_6. 1 hit.
PF16866. PHD_4. 1 hit.
PF02008. zf-CXXC. 1 hit.
[Graphical view]
SMARTiSM00256. FBOX. 1 hit.
SM00558. JmjC. 1 hit.
SM00367. LRR_CC. 5 hits.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51058. ZF_CXXC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiJHD1_DROME
AccessioniPrimary (citable) accession number: Q9VHH9
Secondary accession number(s): Q7YU79
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: March 7, 2006
Last modified: November 30, 2016
This is version 131 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programDrosophila annotation project

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Drosophila
    Drosophila: entries, gene names and cross-references to FlyBase
  2. SIMILARITY comments
    Index of protein domains and families

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.