Q5NCY0 (KDM6B_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lysine-specific demethylase 6B
EC=1.14.11.-

Alternative name(s):
JmjC domain-containing protein 3
Jumonji domain-containing protein 3

Gene names

Name:	Kdm6b
Synonyms:	Jmjd3, Kiaa0346

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	1641 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation. Ref.5
Cofactor	Ascorbate By similarity. Fe2+ By similarity.
Subunit structure	Interacts with TLE1 By similarity. Component of the MLL4 complex, at least composed of MLL4, ASH2L, RBBP5, WDR5, and KDM6B By similarity.
Subcellular location	Nucleus By similarity.
Induction	By inflammatory stimuli; mediated by NF-kappa-B. Ref.5
Sequence similarities	Belongs to the UTX family. Contains 1 JmjC domain.
Sequence caution	The sequence BAE22775.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Inflammatory response
Cellular component	Nucleus
Ligand	Iron Metal-binding
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	histone demethylation Inferred from mutant phenotype. Source: MGI inflammatory response Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of transcription from RNA polymerase II promoter Inferred from direct assay. Source: MGI
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding Inferred from direct assay. Source: MGI
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1641	1641	Lysine-specific demethylase 6B		PRO_0000292008
Regions
	Domain	1337 – 1500	164	JmjC
	Compositional bias	32 – 85	54	Pro-rich
	Compositional bias	195 – 908	714	Pro-rich
	Compositional bias	370 – 408	39	Ser-rich
	Compositional bias	743 – 766	24	Thr-rich
	Compositional bias	1045 – 1080	36	Pro-rich
Sites
	Metal binding	1388	1	Iron By similarity
	Metal binding	1390	1	Iron By similarity
Experimental info
	Sequence conflict	172	1	P → S in AAH75632. Ref.2
	Sequence conflict	965	1	A → T in BAC97931. Ref.3
	Sequence conflict	1290	1	L → LQ in BAC97931. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Q5NCY0 [UniParc]. Last modified February 1, 2005. Version 1. Checksum: 6CBE3620998427EA	FASTA	1,641	176,355
	10 20 30 40 50 60 MHRAVDPPGA RSAREAFALG GLSCAGAWSS CPPHPPPRSS WLPGGRCSAS VGQPPLSAPL 70 80 90 100 110 120 PPSHGSSSGH PNKPYYAPGT PTPRPLHGKL ESLHGCVQAL LREPAQPGLW EQLGQLYESE 130 140 150 160 170 180 HDSEEAVCCY HRALRYGGSF AELGPRIGRL QQAQLWNFHA GSCQHRAKVL PPLEQVWNLL 190 200 210 220 230 240 HLEHKRNYGA KRGGPPVKRS AEPPVVQPMP PAALSGPSGE EGLSPGGKRR RGCSSEQAGL 250 260 270 280 290 300 PPGLPLPPPP PPPPPPPPPP PPPPPPLPGL AISPPFQLTK PGLWNTLHGD AWGPERKGSA 310 320 330 340 350 360 PPERQEQRHS MPHSYPYPAP AYSAHPPSHR LVPNTPLGPG PRPPGAESHG CLPATRPPGS 370 380 390 400 410 420 DLRESRVQRS RMDSSVSPAA STACVPYAPS RPPGLPGTSS SSSSSSSSNN TGLRGVEPSP 430 440 450 460 470 480 GIPGADHYQN PALEISPHQA RLGPSAHSSR KPFLTAPAAT PHLSLPPGTP SSPPPPCPRL 490 500 510 520 530 540 LRPPPPPAWM KGSACRAARE DGEILGELFF GAEGPPRPPP PPLPHRDGFL GPPNPRFSVG 550 560 570 580 590 600 TQDSHNPPIP PTTTSSSSSS NSHSSSPTGP VPFPPPSYLA RSIDPLPRPS SPTLSPQDPP 610 620 630 640 650 660 LPPLTLALPP APPSSCHQNT SGSFRRSESP RPRVSFPKTP EVGQGPPPGP VSKAPQPVPP 670 680 690 700 710 720 GVGELPARGP RLFDFPPTPL EDQFEEPAEF KILPDGLANI MKMLDESIRK EEEQQQQQEA 730 740 750 760 770 780 GVAPPPPLKE PFASLQPPFP SDTAPATTTA APTTATTTTT TTTTTTQEEE KKPPPALPPP 790 800 810 820 830 840 PPLAKFPPPP QPQPPPPPPA SPASLLKSLA SVLEGQKYCY RGTGAAVSTR PGSVPATQYS 850 860 870 880 890 900 PSPASGATAP PPTSVAPSAQ GSPKPSVSSS SQFSTSGGPW AREHRAGEEP APGPVTPAQL 910 920 930 940 950 960 PPPLPLPPAR SESEVLEEIS RACETLVERV GRSAINPVDT ADPVDSGTEP QPPPAQAKEE 970 980 990 1000 1010 1020 SGGVAVAAAG PGSGKRRQKE HRRHRRACRD SVGRRPREGR AKAKAKAPKE KSRRVLGNLD 1030 1040 1050 1060 1070 1080 LQSEEIQGRE KARPDVGGVS KVKTPTAPAP PPAPAPAAQP TPPSAPVPGK KTREEAPGPP 1090 1100 1110 1120 1130 1140 GVSRADMLKL RSLSEGPPKE LKIRLIKVES GDKETFIASE VEERRLRMAD LTISHCAADV 1150 1160 1170 1180 1190 1200 MRASKNAKVK GKFRESYLSP AQSVKPKINT EEKLPREKLN PPTPSIYLES KRDAFSPVLL 1210 1220 1230 1240 1250 1260 QFCTDPRNPI TVIRGLAGSL RLNLGLFSTK TLVEASGEHT VEVRTQVQQP SDENWDLTGT 1270 1280 1290 1300 1310 1320 RQIWPCESSR SHTTIAKYAQ YQASSFQESL QEERESEDEE SEEPDSTTGT SPSSAPDPKN 1330 1340 1350 1360 1370 1380 HHIIKFGTNI DLSDAKRWKP QLQELLKLPA FMRVTSTGNM LSHVGHTILG MNTVQLYMKV 1390 1400 1410 1420 1430 1440 PGSRTPGHQE NNNFCSVNIN IGPGDCEWFA VHEHYWETIS AFCDRHGVDY LTGSWWPILD 1450 1460 1470 1480 1490 1500 DLYASNIPVY RFVQRPGDLV WINAGTVHWV QATGWCNNIA WNVGPLTAYQ YQLALERYEW 1510 1520 1530 1540 1550 1560 NEVKNVKSIV PMIHVSWNVA RTVKISDPDL FKMIKFCLLQ SMKHCQVQRE SLVRAGKKIA 1570 1580 1590 1600 1610 1620 YQGRVKDEPA YYCNECDVEV FNILFVTSEN GSRNTYLVHC EGCARRRSAG LQGVVVLEQY 1630 1640 RTEELAQAYD AFTLAPASTS R

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed: 19468303] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: C57BL/6J.
[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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: C57BL/6. Tissue: Brain.
[3]	"Prediction of the coding sequences of mouse homologues of KIAA gene: III. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries." Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H. DNA Res. 10:167-180(2003) [PubMed: 14621295] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 935-1641. Tissue: Embryonic tail.
[4]	"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: 16141072] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1138-1641. Strain: C57BL/6J. Tissue: Egg.
[5]	"The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing." De Santa F., Totaro M.G., Prosperini E., Notarbartolo S., Testa G., Natoli G. Cell 130:1083-1094(2007) [PubMed: 17825402] [Abstract] Cited for: FUNCTION, INDUCTION.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AL596125 Genomic DNA. Translation: CAI35996.1. BC075632 mRNA. Translation: AAH75632.1. AK129121 mRNA. Translation: BAC97931.1. AK136019 mRNA. Translation: BAE22775.1. Different initiation.
IPI	IPI00420594.
RefSeq	NP_001017426.1. NM_001017426.1.
UniGene	Mm.261201. Mm.472522.
3D structure databases
ProteinModelPortal	Q5NCY0.
SMR	Q5NCY0. Positions 73-141, 1176-1494.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-39160N.
IntAct	Q5NCY0. 3 interactions.
STRING	Q5NCY0.
PTM databases
PhosphoSite	Q5NCY0.
Proteomic databases
PRIDE	Q5NCY0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000094077; ENSMUSP00000091620; ENSMUSG00000018476.
GeneID	216850.
KEGG	mmu:216850.
UCSC	uc007jqd.1. mouse.
Organism-specific databases
CTD	23135.
MGI	MGI:2448492. Kdm6b.
Rouge	Search...
Phylogenomic databases
eggNOG	roNOG12400.
InParanoid	Q5NCY0.
OMA	LSCAGAW.
OrthoDB	EOG402WRG.
Gene expression databases
ArrayExpress	Q5NCY0.
Bgee	Q5NCY0.
CleanEx	MM_JMJD3.
Genevestigator	Q5NCY0.
Family and domain databases
InterPro	IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR011990. TPR-like_helical. [Graphical view]
Gene3D	G3DSA:1.25.40.10. TPR-like_helical. 1 hit.
KO	K11448.
Pfam	PF02373. JmjC. 1 hit. [Graphical view]
SMART	SM00558. JmjC. 1 hit. [Graphical view]
PROSITE	PS51184. JMJC. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	375392.
SOURCE	Search...

Entry information

Entry name

KDM6B_MOUSE

Accession

Primary (citable) accession number: Q5NCY0
Secondary accession number(s): Q3UWY9, Q4VC26, Q6ZQD3

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 26, 2007
Last sequence update:	February 1, 2005
Last modified:	November 16, 2011
This is version 57 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program