Reviewed, UniProtKB/Swiss-Prot Q6P1G2 (KDM2B_MOUSE)

Names and origin

Protein names

Recommended name:
    Lysine-specific demethylase 2B
    EC=1.14.11.27
Alternative name(s):
    JmjC domain-containing histone demethylation protein 1B
    [Histone-H3]-lysine-36 demethylase 1B
    F-box and leucine-rich repeat protein 10
    F-box/LRR-repeat protein 10
    F-box protein FBL10

Gene names

Name:	Kdm2b
Synonyms:	Fbl10, Fbxl10, Jhdm1b, Kiaa3014

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

Protein attributes

Sequence length	1309 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation. May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex By similarity.
Catalytic activity	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.
Cofactor	Binds 1 Fe2+ ion per subunit By similarity.
Subunit structure	Directly interacts with SKP1A and CUL1 By similarity.
Subcellular location	Nucleus › nucleolus By similarity.
Domain	The JmjC domain mediates demethylation activity. It is also required for repression of ribosomal RNA genes By similarity.
Sequence similarities	Belongs to the JHDM1 histone demethylase family. Contains 1 CXXC-type zinc finger. Contains 1 F-box domain. Contains 1 JmjC domain. Contains 4 LRR (leucine-rich) repeats. Contains 1 PHD-type zinc finger.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Ubl conjugation pathway
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil Leucine-rich repeat Repeat Zinc-finger
Ligand	Iron Metal-binding RNA-binding Zinc rRNA-binding
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase Repressor
PTM	Phosphoprotein
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW modification-dependent protein catabolic process Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	DNA binding Inferred from electronic annotation. Source: InterPro histone demethylase activity (H3-K36 specific) Inferred from electronic annotation. Source: EC iron 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 protein binding Inferred from physical interaction. Source: IntAct zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
Rnf2	Q9CQJ4	1	EBI-1216214,EBI-927321

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q6P1G2-1)

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.

Isoform 2 (identifier: Q6P1G2-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-533: Missing.
     534-551: TLAITGVPVVSWPKKTAK → MAMSVSAEDDDYESEPDQ

Isoform 3 (identifier: Q6P1G2-3)

The sequence of this isoform differs from the canonical sequence as follows:
     627-656: PVLPHTAVCLVCGEAGKEDTVEEEEGKFNL → VSAQKAQAGLMQGLPAICPALGLLCGMGEV
     657-1309: Missing.

Note: No experimental confirmation available.

Isoform 4 (identifier: Q6P1G2-4)

The sequence of this isoform differs from the canonical sequence as follows:
     2-1196: Missing.

Note: No experimental confirmation available.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1309	1309	Lysine-specific demethylase 2B		PRO_0000119854
Regions
	Domain	147 – 315	169	JmjC
	Domain	1032 – 1078	47	F-box
	Repeat	1121 – 1144	24	LRR 1
	Repeat	1185 – 1208	24	LRR 2
	Repeat	1242 – 1266	25	LRR 3
	Repeat	1267 – 1309	43	LRR 4
	Zinc finger	579 – 625	47	CXXC-type
	Zinc finger	632 – 698	67	PHD-type
	Coiled coil	916 – 944	29	Potential
	Compositional bias	378 – 403	26	Glu-rich
Sites
	Metal binding	211	1	Iron; catalytic By similarity
	Metal binding	213	1	Iron; catalytic By similarity
	Metal binding	283	1	Iron; catalytic By similarity
	Binding site	208	1	Substrate By similarity
	Binding site	228	1	Substrate By similarity
Amino acid modifications
	Modified residue	192	1	Phosphotyrosine By similarity
	Modified residue	447	1	Phosphoserine By similarity
	Modified residue	470	1	Phosphoserine By similarity
Natural variations
	Alternative sequence	1 – 533	533	Missing in isoform 2.		VSP_011342
	Alternative sequence	2 – 1196	1195	Missing in isoform 4.		VSP_019003
	Alternative sequence	534 – 551	18	TLAIT…KKTAK → MAMSVSAEDDDYESEPDQ in isoform 2.		VSP_011343
	Alternative sequence	627 – 656	30	PVLPH…GKFNL → VSAQKAQAGLMQGLPAICPA LGLLCGMGEV in isoform 3.		VSP_017477
	Alternative sequence	657 – 1309	653	Missing in isoform 3.		VSP_017478
Experimental info
	Sequence conflict	461	1	T → M in BAC98289. Ref.3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 5BD203C3535C4D88	FASTA	1,309	149,733
	10 20 30 40 50 60 MEAEKDSGRR LRAIDRQRYD ENEDLSDVEE IVSVRGFSLE EKLRSQLYQG DFVHAMEGKD 70 80 90 100 110 120 FNYEYVQREA LRVPLVFRDK DGLGIKMPDP DFTVRDVKLL VGSRRLVDVM DVNTQKGTEM 130 140 150 160 170 180 SMSQFVRYYE TPEAQRDKLY NVISLEFSHT KLEHLVKRPT VVDLVDWVDN MWPQHLKEKQ 190 200 210 220 230 240 TEATNALAEM KYPKVKKYCL MSVKGCFTDF HIDFGGTSVW YHVFRGGKIF WLIPPTLHNL 250 260 270 280 290 300 ALYEEWVLSG KQSDIFLGDR VERCQRIELK QGYTFFIPSG WIHAVYTPVD SLVFGGNILH 310 320 330 340 350 360 SFNVPMQLRI YEIEDRTRVQ PKFRYPFYYE MCWYVLERYV YCVTQRSYLT QEYQRELMLI 370 380 390 400 410 420 DAPRKTSVDG FSSDSWLDME EESCEQQPQE EEEEEEDKEE EGDGADKTPK PPTDDPTSPT 430 440 450 460 470 480 STPPEDQDST GKKPKAPAIR FLKRTLSNES EESVKSTSMP TDDPKTPTGS PATEVSTKWT 490 500 510 520 530 540 HLTEFELKGL KALVEKLESL PENKKCVPEG IEDPQALLEG VKNVLKEHVD DDPTLAITGV 550 560 570 580 590 600 PVVSWPKKTA KNRVVGRPKG KLGPASAVKL AANRTTAGAR RRRTRCRKCE ACLRTECGEC 610 620 630 640 650 660 HFCKDMKKFG GPGRMKQSCI MRQCIAPVLP HTAVCLVCGE AGKEDTVEEE EGKFNLMLME 670 680 690 700 710 720 CSICNEIIHP GCLKIKESEG VVNDELPNCW ECPKCNHAGK TGKQKRGPGF KYASNLPGSL 730 740 750 760 770 780 LKEQKMNRDN KEGQEPAKRR SECEEAPRRR SDEHPKKVPA DGILRRKSDD VHLRRKRKYE 790 800 810 820 830 840 KPQELSGRKR ASSLQTSPGS SSHLSPRPPL GSSLSPWWRS SLTYFQQQLK PGKEDKLFRK 850 860 870 880 890 900 KRRSWKNAED RLSLANKPLR RFKQEPEDDL PEAPPKTRES DQSRSSSPTA GPSTEGAEGP 910 920 930 940 950 960 EEKKKVKMRR KRRLVNKELS KELSKELNHE IQKTESTLAH ESQQPIKSEP ESENDEPKRP 970 980 990 1000 1010 1020 LSHCERPHRF SKGLNGTPRE LRHSLGPGLR SPPRVMSRPP PSASPPKCIQ MERHVIRPPP 1030 1040 1050 1060 1070 1080 ISPPPDSLPL DDGAAHVMHR EVWMAVFSYL SHRDLCVCMR VCRTWNRWCC DKRLWTRIDL 1090 1100 1110 1120 1130 1140 NRCKSITPLM LSGIIRRQPV SLDLSWTNIS KKQLSWLINR LPGLRDLVLS GCSWIAVSAL 1150 1160 1170 1180 1190 1200 CSSSCPLLRT LDVQWVEGLK DAQMRDLLSP PTDNRPGQMD NRSKLRNIVE LRLAGLDITD 1210 1220 1230 1240 1250 1260 VSLRLIIRHM PLLSKLQLSY CNHINDQSIN LLTAVGTTTR DSLTEVNLSD CNKVTDLCLS 1270 1280 1290 1300 FFKRCGNICH IDLRYCKQVT KEGCEQFIAE MSVSVQFGQV EEKLLQKLS
	Isoform 2. Checksum: EA6E56115E4B550E	FASTA	776	88,005
	10 20 30 40 50 60 MAMSVSAEDD DYESEPDQNR VVGRPKGKLG PASAVKLAAN RTTAGARRRR TRCRKCEACL 70 80 90 100 110 120 RTECGECHFC KDMKKFGGPG RMKQSCIMRQ CIAPVLPHTA VCLVCGEAGK EDTVEEEEGK 130 140 150 160 170 180 FNLMLMECSI CNEIIHPGCL KIKESEGVVN DELPNCWECP KCNHAGKTGK QKRGPGFKYA 190 200 210 220 230 240 SNLPGSLLKE QKMNRDNKEG QEPAKRRSEC EEAPRRRSDE HPKKVPADGI LRRKSDDVHL 250 260 270 280 290 300 RRKRKYEKPQ ELSGRKRASS LQTSPGSSSH LSPRPPLGSS LSPWWRSSLT YFQQQLKPGK 310 320 330 340 350 360 EDKLFRKKRR SWKNAEDRLS LANKPLRRFK QEPEDDLPEA PPKTRESDQS RSSSPTAGPS 370 380 390 400 410 420 TEGAEGPEEK KKVKMRRKRR LVNKELSKEL SKELNHEIQK TESTLAHESQ QPIKSEPESE 430 440 450 460 470 480 NDEPKRPLSH CERPHRFSKG LNGTPRELRH SLGPGLRSPP RVMSRPPPSA SPPKCIQMER 490 500 510 520 530 540 HVIRPPPISP PPDSLPLDDG AAHVMHREVW MAVFSYLSHR DLCVCMRVCR TWNRWCCDKR 550 560 570 580 590 600 LWTRIDLNRC KSITPLMLSG IIRRQPVSLD LSWTNISKKQ LSWLINRLPG LRDLVLSGCS 610 620 630 640 650 660 WIAVSALCSS SCPLLRTLDV QWVEGLKDAQ MRDLLSPPTD NRPGQMDNRS KLRNIVELRL 670 680 690 700 710 720 AGLDITDVSL RLIIRHMPLL SKLQLSYCNH INDQSINLLT AVGTTTRDSL TEVNLSDCNK 730 740 750 760 770 VTDLCLSFFK RCGNICHIDL RYCKQVTKEG CEQFIAEMSV SVQFGQVEEK LLQKLS
	Isoform 3. Checksum: F2917493A7697ED2	FASTA	656	74,951
	10 20 30 40 50 60 MEAEKDSGRR LRAIDRQRYD ENEDLSDVEE IVSVRGFSLE EKLRSQLYQG DFVHAMEGKD 70 80 90 100 110 120 FNYEYVQREA LRVPLVFRDK DGLGIKMPDP DFTVRDVKLL VGSRRLVDVM DVNTQKGTEM 130 140 150 160 170 180 SMSQFVRYYE TPEAQRDKLY NVISLEFSHT KLEHLVKRPT VVDLVDWVDN MWPQHLKEKQ 190 200 210 220 230 240 TEATNALAEM KYPKVKKYCL MSVKGCFTDF HIDFGGTSVW YHVFRGGKIF WLIPPTLHNL 250 260 270 280 290 300 ALYEEWVLSG KQSDIFLGDR VERCQRIELK QGYTFFIPSG WIHAVYTPVD SLVFGGNILH 310 320 330 340 350 360 SFNVPMQLRI YEIEDRTRVQ PKFRYPFYYE MCWYVLERYV YCVTQRSYLT QEYQRELMLI 370 380 390 400 410 420 DAPRKTSVDG FSSDSWLDME EESCEQQPQE EEEEEEDKEE EGDGADKTPK PPTDDPTSPT 430 440 450 460 470 480 STPPEDQDST GKKPKAPAIR FLKRTLSNES EESVKSTSMP TDDPKTPTGS PATEVSTKWT 490 500 510 520 530 540 HLTEFELKGL KALVEKLESL PENKKCVPEG IEDPQALLEG VKNVLKEHVD DDPTLAITGV 550 560 570 580 590 600 PVVSWPKKTA KNRVVGRPKG KLGPASAVKL AANRTTAGAR RRRTRCRKCE ACLRTECGEC 610 620 630 640 650 HFCKDMKKFG GPGRMKQSCI MRQCIAVSAQ KAQAGLMQGL PAICPALGLL CGMGEV
	Isoform 4. Checksum: FF378CEB4B3674FE	FASTA	114	12,956
	10 20 30 40 50 60 MDITDVSLRL IIRHMPLLSK LQLSYCNHIN DQSINLLTAV GTTTRDSLTE VNLSDCNKVT 70 80 90 100 110 DLCLSFFKRC GNICHIDLRY CKQVTKEGCE QFIAEMSVSV QFGQVEEKLL QKLS

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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: 16141072] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 3 AND 4). Strain: C57BL/6J. Tissue: Cerebellum and Embryo.
[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] (ISOFORMS 1 AND 2). 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 6-1309 (ISOFORM 1). Tissue: Brain.
[4]	"A family of mammalian F-box proteins." Winston J.T., Koepp D.M., Zhu C., Elledge S.J., Harper J.W. Curr. Biol. 9:1180-1182(1999) [PubMed: 10531037] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 1011-1309 (ISOFORMS 1/2).
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AK012952 mRNA. Translation: BAB28568.2. AK043352 mRNA. Translation: BAE20639.1. BC057622 mRNA. Translation: AAH57622.1. BC065090 mRNA. Translation: AAH65090.1. AK129479 mRNA. Translation: BAC98289.1. AF176524 mRNA. Translation: AAF09133.1.
IPI	IPI00420248. IPI00457832. IPI00742387. IPI00853681.
RefSeq	NP_001003953.1. NP_001005866.1. NP_038938.1.
UniGene	Mm.86406
3D structure databases
SMR	Q6P1G2. Positions 35-361.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q6P1G2. 11 interactions.
PTM databases
PhosphoSite	Q6P1G2.
Proteomic databases
PRIDE	Q6P1G2.
Genome annotation databases
Ensembl	ENSMUSG00000029475. Mus musculus. [Contig view]
GeneID	30841.
KEGG	mmu:30841.
Organism-specific databases
MGI	MGI:1354737. Kdm2b.
Rouge	Search...
Phylogenomic databases
HOGENOM	Q6P1G2.
HOVERGEN	Q6P1G2.
OMA	Q6P1G2. QLKPGKE.
Enzyme and pathway databases
BRENDA	1.14.11.27. 244.
Gene expression databases
Bgee	Q6P1G2.
CleanEx	MM_FBXL10.
GermOnline	ENSMUSG00000029475. Mus musculus.
Family and domain databases
InterPro	IPR001810. F-box. IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. IPR019786. Zinc_finger_PHD-type_CS. IPR002857. Znf_CXXC. IPR001965. Znf_PHD. IPR019787. Znf_PHD-finger. [Graphical view]
Pfam	PF00646. F-box. 1 hit. PF02373. JmjC. 1 hit. PF02008. zf-CXXC. 1 hit. [Graphical view]
SMART	SM00256. FBOX. 1 hit. SM00558. JmjC. 1 hit. SM00249. PHD. 1 hit. [Graphical view]
PROSITE	PS50181. FBOX. False negative. PS51184. JMJC. 1 hit. PS51058. ZF_CXXC. 1 hit. PS01359. ZF_PHD_1. False negative. PS50016. ZF_PHD_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other Resources
NextBio	307252.
SOURCE	Search...

Entry information

Entry name

KDM2B_MOUSE

Accession

Primary (citable) accession number: Q6P1G2
Secondary accession number(s): Q3V396 , Q6PFD0, Q6ZPE8, Q9CSF7, Q9QZN6

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 16, 2004
Last sequence update:	July 5, 2004
Last modified:	June 16, 2009
This is version 63 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)