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Protein

Probable lysine-specific demethylase 4B

Gene

Kdm4B

Organism
Drosophila melanogaster (Fruit fly)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Probable histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate (By similarity).By similarity

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei130 – 1301Alpha-ketoglutarateBy similarity
Metal bindingi186 – 1861Iron; catalyticPROSITE-ProRule annotation
Metal bindingi188 – 1881Iron; catalyticPROSITE-ProRule annotation
Binding sitei196 – 1961Alpha-ketoglutarateBy similarity
Binding sitei204 – 2041Alpha-ketoglutarateBy similarity
Metal bindingi232 – 2321ZincBy similarity
Metal bindingi238 – 2381ZincBy similarity
Metal bindingi274 – 2741Iron; catalyticPROSITE-ProRule annotation
Metal bindingi304 – 3041ZincBy similarity
Metal bindingi306 – 3061ZincBy similarity

GO - Molecular functioni

GO - Biological processi

  • histone demethylation Source: UniProtKB
  • histone H3-K36 demethylation Source: FlyBase
  • histone H3-K9 demethylation Source: FlyBase
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • 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.
1.14.11.B1. 1994.
ReactomeiR-DME-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Probable lysine-specific demethylase 4B (EC:1.14.11.-)
Alternative name(s):
Probable JmjC domain-containing histone demethylation protein 3B
Gene namesi
Name:Kdm4B
ORF Names:CG33182
OrganismiDrosophila melanogaster (Fruit fly)
Taxonomic identifieri7227 [NCBI]
Taxonomic lineageiEukaryotaMetazoaEcdysozoaArthropodaHexapodaInsectaPterygotaNeopteraEndopterygotaDipteraBrachyceraMuscomorphaEphydroideaDrosophilidaeDrosophilaSophophora
Proteomesi
  • UP000000803 Componenti: Chromosome 2R

Organism-specific databases

FlyBaseiFBgn0053182. Kdm4B.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 590590Probable lysine-specific demethylase 4BPRO_0000234380Add
BLAST

Proteomic databases

PaxDbiQ9V6L0.

Expressioni

Gene expression databases

GenevisibleiQ9V6L0. DM.

Interactioni

Protein-protein interaction databases

BioGridi77204. 1 interaction.
STRINGi7227.FBpp0302636.

Structurei

3D structure databases

ProteinModelPortaliQ9V6L0.
SMRiQ9V6L0. Positions 8-334.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini9 – 5143JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini140 – 306167JmjCPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
InParanoidiQ9V6L0.
KOiK06709.
OrthoDBiEOG7TQV03.
PhylomeDBiQ9V6L0.

Family and domain databases

InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9V6L0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKMSEVPRIK VFRPTWEEFK DFPKYVAYME SQGAHKAGLA KVVPPPEWVP
60 70 80 90 100
RRSGYADLDA LNVTIPAPIC QVVTGKQGYY QQINIQKKPL TVKQFSELAS
110 120 130 140 150
TERYATPKHF DFEDLERKYW KNITYVAPIY GADVSGSITD TDQDSWNINR
160 170 180 190 200
LGTILDYVNK DYNIQIDGVN TAYLYFGMWK TTFAWHTEDM DLYSINYLHF
210 220 230 240 250
GAPKTWYVVP PECGRKLEKV ANQYFPASYK NCNAYLRHKM TLISPQILKQ
260 270 280 290 300
HDVPVSKITQ EAGEIMITFP FGYHAGFNHG FNCAESTNFA MERWIEYGKR
310 320 330 340 350
AVQCTCSNDM VKISMDTFVK RFQSDRYDLW MEGRDVGRHP EDPPNAVLSA
360 370 380 390 400
APLPPHLDVL LCDKKMKKQC NPTKAKSFKE RNPDLDLDEI QQNPNVPDDV
410 420 430 440 450
KAMLKESVLT LDTGDLATDE ADFPNEDAMS LQSPANLKTK QELLEYIDDG
460 470 480 490 500
TEDDDEEEDF KRRKQKRRYD ADYDDDWLAS KRKTNSRNNR GRSPRTKDDR
510 520 530 540 550
SISPASSTSS TSRGARRGKA SGTPRKTPAR RKKDSITTSP AVSSAATAVK
560 570 580 590
TPTSAVVAGT TSIATTTTPP ADGGGGESSS LGSHCTTASP
Length:590
Mass (Da):66,437
Last modified:January 15, 2008 - v3
Checksum:iE7B8C1CB3FA88F75
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE013599 Genomic DNA. Translation: AAF58413.3.
RefSeqiNP_001163137.1. NM_001169666.2.
NP_001163138.1. NM_001169667.2.
NP_001163139.1. NM_001169668.2.
NP_788344.2. NM_176164.4.
UniGeneiDm.6975.

Genome annotation databases

EnsemblMetazoaiFBtr0087770; FBpp0086883; FBgn0053182.
FBtr0302052; FBpp0291262; FBgn0053182.
FBtr0302053; FBpp0291263; FBgn0053182.
FBtr0302054; FBpp0291264; FBgn0053182.
GeneIDi318918.
KEGGidme:Dmel_CG33182.
UCSCiCG33182-RA. d. melanogaster.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE013599 Genomic DNA. Translation: AAF58413.3.
RefSeqiNP_001163137.1. NM_001169666.2.
NP_001163138.1. NM_001169667.2.
NP_001163139.1. NM_001169668.2.
NP_788344.2. NM_176164.4.
UniGeneiDm.6975.

3D structure databases

ProteinModelPortaliQ9V6L0.
SMRiQ9V6L0. Positions 8-334.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi77204. 1 interaction.
STRINGi7227.FBpp0302636.

Proteomic databases

PaxDbiQ9V6L0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblMetazoaiFBtr0087770; FBpp0086883; FBgn0053182.
FBtr0302052; FBpp0291262; FBgn0053182.
FBtr0302053; FBpp0291263; FBgn0053182.
FBtr0302054; FBpp0291264; FBgn0053182.
GeneIDi318918.
KEGGidme:Dmel_CG33182.
UCSCiCG33182-RA. d. melanogaster.

Organism-specific databases

CTDi23030.
FlyBaseiFBgn0053182. Kdm4B.

Phylogenomic databases

eggNOGiKOG0958. Eukaryota.
ENOG410XP0T. LUCA.
GeneTreeiENSGT00530000063342.
InParanoidiQ9V6L0.
KOiK06709.
OrthoDBiEOG7TQV03.
PhylomeDBiQ9V6L0.

Enzyme and pathway databases

BRENDAi1.14.11.27. 1994.
1.14.11.B1. 1994.
ReactomeiR-DME-3214842. HDMs demethylate histones.

Miscellaneous databases

GenomeRNAii318918.
PROiQ9V6L0.

Gene expression databases

GenevisibleiQ9V6L0. DM.

Family and domain databases

InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Drosophila melanogaster."
    Adams M.D., Celniker S.E., Holt R.A., Evans C.A., Gocayne J.D., Amanatides P.G., Scherer S.E., Li P.W., Hoskins R.A., Galle R.F., George R.A., Lewis S.E., Richards S., Ashburner M., Henderson S.N., Sutton G.G., Wortman J.R., Yandell M.D.
    , Zhang Q., Chen L.X., Brandon R.C., Rogers Y.-H.C., Blazej R.G., Champe M., Pfeiffer B.D., Wan K.H., Doyle C., Baxter E.G., Helt G., Nelson C.R., Miklos G.L.G., Abril J.F., Agbayani A., An H.-J., Andrews-Pfannkoch C., Baldwin D., Ballew R.M., Basu A., Baxendale J., Bayraktaroglu L., Beasley E.M., Beeson K.Y., Benos P.V., Berman B.P., Bhandari D., Bolshakov S., Borkova D., Botchan M.R., Bouck J., Brokstein P., Brottier P., Burtis K.C., Busam D.A., Butler H., Cadieu E., Center A., Chandra I., Cherry J.M., Cawley S., Dahlke C., Davenport L.B., Davies P., de Pablos B., Delcher A., Deng Z., Mays A.D., Dew I., Dietz S.M., Dodson K., Doup L.E., Downes M., Dugan-Rocha S., Dunkov B.C., Dunn P., Durbin K.J., Evangelista C.C., Ferraz C., Ferriera S., Fleischmann W., Fosler C., Gabrielian A.E., Garg N.S., Gelbart W.M., Glasser K., Glodek A., Gong F., Gorrell J.H., Gu Z., Guan P., Harris M., Harris N.L., Harvey D.A., Heiman T.J., Hernandez J.R., Houck J., Hostin D., Houston K.A., Howland T.J., Wei M.-H., Ibegwam C., Jalali M., Kalush F., Karpen G.H., Ke Z., Kennison J.A., Ketchum K.A., Kimmel B.E., Kodira C.D., Kraft C.L., Kravitz S., Kulp D., Lai Z., Lasko P., Lei Y., Levitsky A.A., Li J.H., Li Z., Liang Y., Lin X., Liu X., Mattei B., McIntosh T.C., McLeod M.P., McPherson D., Merkulov G., Milshina N.V., Mobarry C., Morris J., Moshrefi A., Mount S.M., Moy M., Murphy B., Murphy L., Muzny D.M., Nelson D.L., Nelson D.R., Nelson K.A., Nixon K., Nusskern D.R., Pacleb J.M., Palazzolo M., Pittman G.S., Pan S., Pollard J., Puri V., Reese M.G., Reinert K., Remington K., Saunders R.D.C., Scheeler F., Shen H., Shue B.C., Siden-Kiamos I., Simpson M., Skupski M.P., Smith T.J., Spier E., Spradling A.C., Stapleton M., Strong R., Sun E., Svirskas R., Tector C., Turner R., Venter E., Wang A.H., Wang X., Wang Z.-Y., Wassarman D.A., Weinstock G.M., Weissenbach J., Williams S.M., Woodage T., Worley K.C., Wu D., Yang S., Yao Q.A., Ye J., Yeh R.-F., Zaveri J.S., Zhan M., Zhang G., Zhao Q., Zheng L., Zheng X.H., Zhong F.N., Zhong W., Zhou X., Zhu S.C., Zhu X., Smith H.O., Gibbs R.A., Myers E.W., Rubin G.M., Venter J.C.
    Science 287:2185-2195(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Berkeley.
  2. Cited for: GENOME REANNOTATION.
    Strain: Berkeley.

Entry informationi

Entry nameiKDM4B_DROME
AccessioniPrimary (citable) accession number: Q9V6L0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: January 15, 2008
Last modified: June 8, 2016
This is version 103 of the entry and version 3 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.