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Protein

Lysine-specific demethylase 4B

Gene

Kdm4b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

Histone demethylase that specifically demethylates 'Lys-9' of histone H3, thereby playing a role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27', H3 'Lys-36' nor H4 'Lys-20'. Only able to demethylate trimethylated H3 'Lys-9', with a weaker activity than KDM4A, KDM4C and KDM4D. 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 sitei133 – 1331Alpha-ketoglutarateBy similarity
Metal bindingi189 – 1891Iron; catalyticPROSITE-ProRule annotation
Metal bindingi191 – 1911Iron; catalyticPROSITE-ProRule annotation
Binding sitei199 – 1991Alpha-ketoglutarateBy similarity
Binding sitei207 – 2071Alpha-ketoglutarateBy similarity
Metal bindingi235 – 2351ZincBy similarity
Metal bindingi241 – 2411ZincBy similarity
Metal bindingi277 – 2771Iron; catalyticPROSITE-ProRule annotation
Metal bindingi307 – 3071ZincBy similarity
Metal bindingi309 – 3091ZincBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri719 – 77759PHD-type 1Add
BLAST
Zinc fingeri839 – 89557PHD-type 2Add
BLAST

GO - Molecular functioni

  • dioxygenase activity Source: UniProtKB-KW
  • histone demethylase activity Source: MGI
  • histone demethylase activity (H3-K9 specific) Source: MGI
  • zinc ion binding Source: InterPro

GO - Biological processi

  • histone H3-K36 demethylation Source: MGI
  • histone H3-K9 demethylation Source: MGI
  • negative regulation of histone H3-K9 trimethylation Source: MGI
  • 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

ReactomeiR-MMU-3214842. HDMs demethylate histones.
R-MMU-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 4B (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 3B
Jumonji domain-containing protein 2B
Gene namesi
Name:Kdm4b
Synonyms:Jhdm3b, Jmjd2b
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 17

Organism-specific databases

MGIiMGI:2442355. Kdm4b.

Subcellular locationi

  • Nucleus PROSITE-ProRule annotation

GO - Cellular componenti

  • cytoplasm Source: MGI
  • nuclear pericentric heterochromatin Source: MGI
  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10861086Lysine-specific demethylase 4BPRO_0000183176Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei599 – 5991N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

EPDiQ91VY5.
MaxQBiQ91VY5.
PaxDbiQ91VY5.
PeptideAtlasiQ91VY5.
PRIDEiQ91VY5.

PTM databases

iPTMnetiQ91VY5.
PhosphoSiteiQ91VY5.

Expressioni

Gene expression databases

BgeeiQ91VY5.
CleanExiMM_JMJD2B.
ExpressionAtlasiQ91VY5. baseline and differential.
GenevisibleiQ91VY5. MM.

Interactioni

Protein-protein interaction databases

BioGridi228758. 6 interactions.
STRINGi10090.ENSMUSP00000025036.

Structurei

3D structure databases

ProteinModelPortaliQ91VY5.
SMRiQ91VY5. Positions 9-337, 905-1022.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini15 – 5743JmjNPROSITE-ProRule annotationAdd
BLAST
Domaini146 – 309164JmjCPROSITE-ProRule annotationAdd
BLAST
Domaini905 – 96258Tudor 1Add
BLAST
Domaini963 – 101957Tudor 2Add
BLAST

Domaini

The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails (By similarity).By similarity

Sequence similaritiesi

Belongs to the JHDM3 histone demethylase family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 2 PHD-type zinc fingers.Curated
Contains 2 Tudor domains.Curated

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri719 – 77759PHD-type 1Add
BLAST
Zinc fingeri839 – 89557PHD-type 2Add
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ91VY5.
KOiK06709.
OMAiYLAIMES.
OrthoDBiEOG7TQV03.
PhylomeDBiQ91VY5.
TreeFamiTF106449.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q91VY5-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MGSEDHSAQN PSCKIMTFRP TMDEFRDFNR YVAYIESQGA HRAGLAKIIP
60 70 80 90 100
PKEWKPRQTY DDIDDVVIPA PIQQVVTGQS GLFTQYNIQK KAMTVGEYRR
110 120 130 140 150
LANSEKYCTP RHQDFDDLER KYWKNLTFVS PIYGADISGS LYDDDVAQWN
160 170 180 190 200
IGNLRTILDM VERECGTIIE GVNTPYLYFG MWKTTFAWHT EDMDLYSINY
210 220 230 240 250
LHFGEPKSWY AIPPEHGKRL ERLAIGFFPG SSQGCDAFLR HKMTLISPII
260 270 280 290 300
LKKYGIPFSR ITQEAGEFMI TFPYGYHAGF NHGFNCAEST NFATLRWIDY
310 320 330 340 350
GKVATQCTCR KDMVKISMDV FVRILQPERY EQWKQGRDLT VLDHTRPTAL
360 370 380 390 400
SSPELSSWSA SRTSIKAKLL RRQISVKESR PWRKAEEERR REPTRRPGPA
410 420 430 440 450
SHRRRSQPKK SKPEESRSPG EATAGVSTLD EARGCSRGEA MPEDEEEEEL
460 470 480 490 500
LPSQGHEAEG VEEDGRGKPR PTKARNKKKT PSPSSPPLLS APPALFPTEE
510 520 530 540 550
VLRPPPQPKS PGPAMGPMAA EGGPPPTPLN VVPPGAPVEE AEVRPRPIIP
560 570 580 590 600
MLYVLPRTSS TDGDREHSAH AQLAPMELGP EEENQAQAGD SQGTTPFSKL
610 620 630 640 650
KVEIKKSRRH PLGRPPTRSP LSVVKQEASS DEEAFLFSGE DDVTDPEALR
660 670 680 690 700
SLLSLQWKNK AASFQAERKF NAAAALSEPY CAICTLFYPY SQSVQTERDS
710 720 730 740 750
AVQPPSKSGQ RTRPLIPEMC FTSSGENTEP LPANSYVGED GTSPLISCAH
760 770 780 790 800
CCLQVHASCY GVRPELAKEG WTCSRCAAHA WTAECCLCNL RGGALQRTTE
810 820 830 840 850
HRWIHVICAI AVPEVRFLNV IERNPVDVSA IPEQRWKLKC IYCRKRMKRV
860 870 880 890 900
SGACIQCSYE HCSTSFHVTC AHAAGVLMEP DDWPYVVSIT CLKHRASGAG
910 920 930 940 950
GQLLRTVSLG QIVITKNRNG LYYRCRVIGT TAQTFYEVNF DDGSYSDNLY
960 970 980 990 1000
PESITSRDCL RLGPPPEGEL VELRWTDGNL YRARFISMAT SLIYQVEFED
1010 1020 1030 1040 1050
GSQLTVKRGD IFTLEEELPK RVRSRLSLST GTPQEPSFSG DDVKAAKRPR
1060 1070 1080
VASVLATTTE DTGRSPEYLS FMESLLQAQG RPGAPF
Length:1,086
Mass (Da):121,604
Last modified:December 1, 2001 - v1
Checksum:i5418B6CBF5E14DAA
GO
Isoform 2 (identifier: Q91VY5-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     593-599: Missing.
     940-997: Missing.

Note: No experimental confirmation available.
Show »
Length:1,021
Mass (Da):114,244
Checksum:iF7AD3B067640F8FC
GO

Sequence cautioni

The sequence BAC98043.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti40 – 401A → T in BAE24866 (PubMed:16141072).Curated
Sequence conflicti576 – 5761M → L in AAH05480 (PubMed:15489334).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei593 – 5997Missing in isoform 2. 1 PublicationVSP_018309
Alternative sequencei940 – 99758Missing in isoform 2. 1 PublicationVSP_018310Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129233 mRNA. Translation: BAC98043.1. Different initiation.
AK141879 mRNA. Translation: BAE24866.1.
BC005480 mRNA. Translation: AAH05480.1.
BC007145 mRNA. Translation: AAH07145.1.
CCDSiCCDS28904.1. [Q91VY5-1]
RefSeqiNP_742144.1. NM_172132.2. [Q91VY5-1]
XP_006523956.1. XM_006523893.1. [Q91VY5-1]
UniGeneiMm.45047.

Genome annotation databases

EnsembliENSMUST00000025036; ENSMUSP00000025036; ENSMUSG00000024201. [Q91VY5-1]
GeneIDi193796.
KEGGimmu:193796.
UCSCiuc008dbu.2. mouse. [Q91VY5-2]
uc008dbv.2. mouse. [Q91VY5-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129233 mRNA. Translation: BAC98043.1. Different initiation.
AK141879 mRNA. Translation: BAE24866.1.
BC005480 mRNA. Translation: AAH05480.1.
BC007145 mRNA. Translation: AAH07145.1.
CCDSiCCDS28904.1. [Q91VY5-1]
RefSeqiNP_742144.1. NM_172132.2. [Q91VY5-1]
XP_006523956.1. XM_006523893.1. [Q91VY5-1]
UniGeneiMm.45047.

3D structure databases

ProteinModelPortaliQ91VY5.
SMRiQ91VY5. Positions 9-337, 905-1022.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi228758. 6 interactions.
STRINGi10090.ENSMUSP00000025036.

PTM databases

iPTMnetiQ91VY5.
PhosphoSiteiQ91VY5.

Proteomic databases

EPDiQ91VY5.
MaxQBiQ91VY5.
PaxDbiQ91VY5.
PeptideAtlasiQ91VY5.
PRIDEiQ91VY5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000025036; ENSMUSP00000025036; ENSMUSG00000024201. [Q91VY5-1]
GeneIDi193796.
KEGGimmu:193796.
UCSCiuc008dbu.2. mouse. [Q91VY5-2]
uc008dbv.2. mouse. [Q91VY5-1]

Organism-specific databases

CTDi23030.
MGIiMGI:2442355. Kdm4b.

Phylogenomic databases

eggNOGiENOG410IT40. Eukaryota.
COG5141. LUCA.
GeneTreeiENSGT00530000063342.
HOGENOMiHOG000231125.
InParanoidiQ91VY5.
KOiK06709.
OMAiYLAIMES.
OrthoDBiEOG7TQV03.
PhylomeDBiQ91VY5.
TreeFamiTF106449.

Enzyme and pathway databases

ReactomeiR-MMU-3214842. HDMs demethylate histones.
R-MMU-5693565. Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.

Miscellaneous databases

PROiQ91VY5.
SOURCEiSearch...

Gene expression databases

BgeeiQ91VY5.
CleanExiMM_JMJD2B.
ExpressionAtlasiQ91VY5. baseline and differential.
GenevisibleiQ91VY5. MM.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Strain: C57BL/6J.
    Tissue: Embryonic tail and Spinal ganglion.
  2. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Mammary tumor.

Entry informationi

Entry nameiKDM4B_MOUSE
AccessioniPrimary (citable) accession number: Q91VY5
Secondary accession number(s): Q3UR22, Q6ZQ30, Q99K42
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: December 1, 2001
Last modified: July 6, 2016
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  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.