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Protein

Lysine-specific demethylase 2B

Gene

Kdm2b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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 activityi

Protein N6,N6-dimethyl-L-lysine + 2 2-oxoglutarate + 2 O2 = protein L-lysine + 2 succinate + 2 formaldehyde + 2 CO2.By similarity

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei208SubstrateBy similarity1
Metal bindingi211Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi213Iron; catalyticPROSITE-ProRule annotation1
Binding sitei228SubstrateBy similarity1
Metal bindingi283Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri579 – 625CXXC-typePROSITE-ProRule annotationAdd BLAST47
Zinc fingeri632 – 698PHD-typePROSITE-ProRule annotationAdd BLAST67

GO - Molecular functioni

  • histone demethylase activity Source: BHF-UCL
  • histone demethylase activity (H3-K36 specific) Source: UniProtKB-EC
  • RNA polymerase II proximal promoter sequence-specific DNA binding Source: MGI
  • rRNA binding Source: UniProtKB-KW
  • zinc ion binding Source: InterPro

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase, Repressor, RNA-binding, rRNA-binding
Biological processTranscription, Transcription regulation, Ubl conjugation pathway
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi1.14.11.27 3474
ReactomeiR-MMU-3214842 HDMs demethylate histones

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 2B (EC:1.14.11.27By similarity)
Alternative name(s):
F-box and leucine-rich repeat protein 10
F-box protein FBL10
F-box/LRR-repeat protein 10
JmjC domain-containing histone demethylation protein 1B
[Histone-H3]-lysine-36 demethylase 1B
Gene namesi
Name:Kdm2b
Synonyms:Fbl10, Fbxl10, Jhdm1b, Kiaa3014
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 5

Organism-specific databases

MGIiMGI:1354737 Kdm2b

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001198541 – 1309Lysine-specific demethylase 2BAdd BLAST1309

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei26PhosphoserineBy similarity1
Modified residuei447PhosphoserineBy similarity1
Modified residuei450PhosphoserineBy similarity1
Modified residuei466PhosphothreonineBy similarity1
Modified residuei470PhosphoserineBy similarity1
Cross-linki830Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki863Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei924PhosphoserineBy similarity1
Modified residuei948PhosphoserineBy similarity1
Modified residuei952PhosphoserineBy similarity1
Modified residuei991PhosphoserineBy similarity1
Modified residuei1004PhosphoserineBy similarity1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ6P1G2
PaxDbiQ6P1G2
PeptideAtlasiQ6P1G2
PRIDEiQ6P1G2

PTM databases

iPTMnetiQ6P1G2
PhosphoSitePlusiQ6P1G2

Expressioni

Gene expression databases

BgeeiENSMUSG00000029475 Expressed in 30 organ(s), highest expression level in testis
CleanExiMM_FBXL10
ExpressionAtlasiQ6P1G2 baseline and differential
GenevisibleiQ6P1G2 MM

Interactioni

Subunit structurei

Directly interacts with SKP1 and CUL1.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Rnf2Q9CQJ44EBI-1216214,EBI-927321

Protein-protein interaction databases

BioGridi205978, 19 interactors
DIPiDIP-46351N
IntActiQ6P1G2, 11 interactors
STRINGi10090.ENSMUSP00000038229

Structurei

3D structure databases

ProteinModelPortaliQ6P1G2
SMRiQ6P1G2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini147 – 315JmjCPROSITE-ProRule annotationAdd BLAST169
Domaini1032 – 1078F-boxAdd BLAST47
Repeati1106 – 1127LRR 1Add BLAST22
Repeati1129 – 1155LRR 2Add BLAST27
Repeati1195 – 1220LRR 3Add BLAST26
Repeati1221 – 1250LRR 4Add BLAST30
Repeati1251 – 1275LRR 5Add BLAST25
Repeati1276 – 1309LRR 6Add BLAST34

Coiled coil

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Coiled coili916 – 944Sequence analysisAdd BLAST29

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi378 – 403Glu-richAdd BLAST26

Domaini

The JmjC domain mediates demethylation activity. It is also required for repression of ribosomal RNA genes (By similarity).By similarity

Sequence similaritiesi

Belongs to the JHDM1 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri579 – 625CXXC-typePROSITE-ProRule annotationAdd BLAST47
Zinc fingeri632 – 698PHD-typePROSITE-ProRule annotationAdd BLAST67

Keywords - Domaini

Coiled coil, Leucine-rich repeat, Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
KOG1947 Eukaryota
ENOG410XQXU LUCA
GeneTreeiENSGT00550000074396
HOGENOMiHOG000007396
InParanoidiQ6P1G2
KOiK10276
OrthoDBiEOG091G00M1
PhylomeDBiQ6P1G2
TreeFamiTF106480

Family and domain databases

Gene3Di3.30.40.10, 1 hit
3.80.10.10, 1 hit
InterProiView protein in InterPro
IPR001810 F-box_dom
IPR003347 JmjC_dom
IPR006553 Leu-rich_rpt_Cys-con_subtyp
IPR032675 LRR_dom_sf
IPR002857 Znf_CXXC
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF00646 F-box, 1 hit
PF02373 JmjC, 1 hit
PF16866 PHD_4, 1 hit
PF02008 zf-CXXC, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00367 LRR_CC, 5 hits
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS51058 ZF_CXXC, 1 hit
PS50016 ZF_PHD_2, 1 hit

Sequences (4+)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 4 described isoforms and 7 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q6P1G2-1) [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
MEAEKDSGRR LRAIDRQRYD ENEDLSDVEE IVSVRGFSLE EKLRSQLYQG
60 70 80 90 100
DFVHAMEGKD FNYEYVQREA LRVPLVFRDK DGLGIKMPDP DFTVRDVKLL
110 120 130 140 150
VGSRRLVDVM DVNTQKGTEM SMSQFVRYYE TPEAQRDKLY NVISLEFSHT
160 170 180 190 200
KLEHLVKRPT VVDLVDWVDN MWPQHLKEKQ TEATNALAEM KYPKVKKYCL
210 220 230 240 250
MSVKGCFTDF HIDFGGTSVW YHVFRGGKIF WLIPPTLHNL ALYEEWVLSG
260 270 280 290 300
KQSDIFLGDR VERCQRIELK QGYTFFIPSG WIHAVYTPVD SLVFGGNILH
310 320 330 340 350
SFNVPMQLRI YEIEDRTRVQ PKFRYPFYYE MCWYVLERYV YCVTQRSYLT
360 370 380 390 400
QEYQRELMLI DAPRKTSVDG FSSDSWLDME EESCEQQPQE EEEEEEDKEE
410 420 430 440 450
EGDGADKTPK PPTDDPTSPT STPPEDQDST GKKPKAPAIR FLKRTLSNES
460 470 480 490 500
EESVKSTSMP TDDPKTPTGS PATEVSTKWT HLTEFELKGL KALVEKLESL
510 520 530 540 550
PENKKCVPEG IEDPQALLEG VKNVLKEHVD DDPTLAITGV PVVSWPKKTA
560 570 580 590 600
KNRVVGRPKG KLGPASAVKL AANRTTAGAR RRRTRCRKCE ACLRTECGEC
610 620 630 640 650
HFCKDMKKFG GPGRMKQSCI MRQCIAPVLP HTAVCLVCGE AGKEDTVEEE
660 670 680 690 700
EGKFNLMLME CSICNEIIHP GCLKIKESEG VVNDELPNCW ECPKCNHAGK
710 720 730 740 750
TGKQKRGPGF KYASNLPGSL LKEQKMNRDN KEGQEPAKRR SECEEAPRRR
760 770 780 790 800
SDEHPKKVPA DGILRRKSDD VHLRRKRKYE KPQELSGRKR ASSLQTSPGS
810 820 830 840 850
SSHLSPRPPL GSSLSPWWRS SLTYFQQQLK PGKEDKLFRK KRRSWKNAED
860 870 880 890 900
RLSLANKPLR RFKQEPEDDL PEAPPKTRES DQSRSSSPTA GPSTEGAEGP
910 920 930 940 950
EEKKKVKMRR KRRLVNKELS KELSKELNHE IQKTESTLAH ESQQPIKSEP
960 970 980 990 1000
ESENDEPKRP LSHCERPHRF SKGLNGTPRE LRHSLGPGLR SPPRVMSRPP
1010 1020 1030 1040 1050
PSASPPKCIQ MERHVIRPPP ISPPPDSLPL DDGAAHVMHR EVWMAVFSYL
1060 1070 1080 1090 1100
SHRDLCVCMR VCRTWNRWCC DKRLWTRIDL NRCKSITPLM LSGIIRRQPV
1110 1120 1130 1140 1150
SLDLSWTNIS KKQLSWLINR LPGLRDLVLS GCSWIAVSAL CSSSCPLLRT
1160 1170 1180 1190 1200
LDVQWVEGLK DAQMRDLLSP PTDNRPGQMD NRSKLRNIVE LRLAGLDITD
1210 1220 1230 1240 1250
VSLRLIIRHM PLLSKLQLSY CNHINDQSIN LLTAVGTTTR DSLTEVNLSD
1260 1270 1280 1290 1300
CNKVTDLCLS FFKRCGNICH IDLRYCKQVT KEGCEQFIAE MSVSVQFGQV

EEKLLQKLS
Length:1,309
Mass (Da):149,733
Last modified:July 5, 2004 - v1
Checksum:i5BD203C3535C4D88
GO
Isoform 2 (identifier: Q6P1G2-2) [UniParc]FASTAAdd to basket

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

Show »
Length:776
Mass (Da):88,005
Checksum:iEA6E56115E4B550E
GO
Isoform 3 (identifier: Q6P1G2-3) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:656
Mass (Da):74,951
Checksum:iF2917493A7697ED2
GO
Isoform 4 (identifier: Q6P1G2-4) [UniParc]FASTAAdd to basket

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

Note: No experimental confirmation available.
Show »
Length:114
Mass (Da):12,956
Checksum:iFF378CEB4B3674FE
GO

Computationally mapped potential isoform sequencesi

There are 7 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
D3YVU7D3YVU7_MOUSE
Lysine-specific demethylase 2B
Kdm2b
1,254Annotation score:
E9QL25E9QL25_MOUSE
Lysine-specific demethylase 2B
Kdm2b
1,303Annotation score:
D3YVU4D3YVU4_MOUSE
Lysine-specific demethylase 2B
Kdm2b
1,266Annotation score:
F6QTG9F6QTG9_MOUSE
Lysine-specific demethylase 2B
Kdm2b
296Annotation score:
D3YUE3D3YUE3_MOUSE
Lysine-specific demethylase 2B
Kdm2b
514Annotation score:
D3YV31D3YV31_MOUSE
Lysine-specific demethylase 2B
Kdm2b
286Annotation score:
D6RHM8D6RHM8_MOUSE
Lysine-specific demethylase 2B
Kdm2b
38Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti461T → M in BAC98289 (PubMed:14621295).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0113421 – 533Missing in isoform 2. 1 PublicationAdd BLAST533
Alternative sequenceiVSP_0190032 – 1196Missing in isoform 4. 1 PublicationAdd BLAST1195
Alternative sequenceiVSP_011343534 – 551TLAIT…KKTAK → MAMSVSAEDDDYESEPDQ in isoform 2. 1 PublicationAdd BLAST18
Alternative sequenceiVSP_017477627 – 656PVLPH…GKFNL → VSAQKAQAGLMQGLPAICPA LGLLCGMGEV in isoform 3. 1 PublicationAdd BLAST30
Alternative sequenceiVSP_017478657 – 1309Missing in isoform 3. 1 PublicationAdd BLAST653

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS19657.1 [Q6P1G2-2]
CCDS39259.1 [Q6P1G2-1]
RefSeqiNP_001003953.1, NM_001003953.2 [Q6P1G2-1]
NP_038938.1, NM_013910.2 [Q6P1G2-2]
UniGeneiMm.86406

Genome annotation databases

EnsembliENSMUST00000031435; ENSMUSP00000031435; ENSMUSG00000029475 [Q6P1G2-2]
ENSMUST00000046073; ENSMUSP00000038229; ENSMUSG00000029475 [Q6P1G2-1]
GeneIDi30841
KEGGimmu:30841
UCSCiuc008zmq.2 mouse [Q6P1G2-2]
uc008zms.3 mouse [Q6P1G2-1]
uc008zmu.2 mouse [Q6P1G2-3]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS19657.1 [Q6P1G2-2]
CCDS39259.1 [Q6P1G2-1]
RefSeqiNP_001003953.1, NM_001003953.2 [Q6P1G2-1]
NP_038938.1, NM_013910.2 [Q6P1G2-2]
UniGeneiMm.86406

3D structure databases

ProteinModelPortaliQ6P1G2
SMRiQ6P1G2
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi205978, 19 interactors
DIPiDIP-46351N
IntActiQ6P1G2, 11 interactors
STRINGi10090.ENSMUSP00000038229

PTM databases

iPTMnetiQ6P1G2
PhosphoSitePlusiQ6P1G2

Proteomic databases

EPDiQ6P1G2
PaxDbiQ6P1G2
PeptideAtlasiQ6P1G2
PRIDEiQ6P1G2

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000031435; ENSMUSP00000031435; ENSMUSG00000029475 [Q6P1G2-2]
ENSMUST00000046073; ENSMUSP00000038229; ENSMUSG00000029475 [Q6P1G2-1]
GeneIDi30841
KEGGimmu:30841
UCSCiuc008zmq.2 mouse [Q6P1G2-2]
uc008zms.3 mouse [Q6P1G2-1]
uc008zmu.2 mouse [Q6P1G2-3]

Organism-specific databases

CTDi84678
MGIiMGI:1354737 Kdm2b
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1633 Eukaryota
KOG1947 Eukaryota
ENOG410XQXU LUCA
GeneTreeiENSGT00550000074396
HOGENOMiHOG000007396
InParanoidiQ6P1G2
KOiK10276
OrthoDBiEOG091G00M1
PhylomeDBiQ6P1G2
TreeFamiTF106480

Enzyme and pathway databases

BRENDAi1.14.11.27 3474
ReactomeiR-MMU-3214842 HDMs demethylate histones

Miscellaneous databases

PROiPR:Q6P1G2
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000029475 Expressed in 30 organ(s), highest expression level in testis
CleanExiMM_FBXL10
ExpressionAtlasiQ6P1G2 baseline and differential
GenevisibleiQ6P1G2 MM

Family and domain databases

Gene3Di3.30.40.10, 1 hit
3.80.10.10, 1 hit
InterProiView protein in InterPro
IPR001810 F-box_dom
IPR003347 JmjC_dom
IPR006553 Leu-rich_rpt_Cys-con_subtyp
IPR032675 LRR_dom_sf
IPR002857 Znf_CXXC
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PfamiView protein in Pfam
PF00646 F-box, 1 hit
PF02373 JmjC, 1 hit
PF16866 PHD_4, 1 hit
PF02008 zf-CXXC, 1 hit
SMARTiView protein in SMART
SM00558 JmjC, 1 hit
SM00367 LRR_CC, 5 hits
SM00249 PHD, 1 hit
SUPFAMiSSF57903 SSF57903, 1 hit
PROSITEiView protein in PROSITE
PS51184 JMJC, 1 hit
PS51058 ZF_CXXC, 1 hit
PS50016 ZF_PHD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiKDM2B_MOUSE
AccessioniPrimary (citable) accession number: Q6P1G2
Secondary accession number(s): Q3V396
, Q6PFD0, Q6ZPE8, Q9CSF7, Q9QZN6
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 16, 2004
Last sequence update: July 5, 2004
Last modified: November 7, 2018
This is version 144 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
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