Q6P1G2 · KDM2B_MOUSE

  • Protein
    Lysine-specific demethylase 2B
  • Gene
    Kdm2b
  • Status
    UniProtKB reviewed (Swiss-Prot)
  • Amino acids
  • Protein existence
    Evidence at protein level
  • Annotation score
    5/5

Function

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 (By similarity).
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

Cofactor

Fe2+ (UniProtKB | Rhea| CHEBI:29033 )

Note: Binds 1 Fe2+ ion per subunit.

Activity regulation

Histone demethylase activity is inhibited by fumarate.

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site208substrate
Binding site211Fe cation (UniProtKB | ChEBI); catalytic
Binding site213Fe cation (UniProtKB | ChEBI); catalytic
Binding site228substrate
Binding site283Fe cation (UniProtKB | ChEBI); catalytic
Binding site586Zn2+ 1 (UniProtKB | ChEBI)
Binding site589Zn2+ 1 (UniProtKB | ChEBI)
Binding site592Zn2+ 1 (UniProtKB | ChEBI)
Binding site597Zn2+ 2 (UniProtKB | ChEBI)
Binding site600Zn2+ 2 (UniProtKB | ChEBI)
Binding site603Zn2+ 2 (UniProtKB | ChEBI)
Binding site619Zn2+ 2 (UniProtKB | ChEBI)
Binding site624Zn2+ 1 (UniProtKB | ChEBI)
Binding site635Zn2+ (UniProtKB | ChEBI)
Binding site638Zn2+ (UniProtKB | ChEBI)
Binding site661Zn2+ (UniProtKB | ChEBI)
Binding site664Zn2+ (UniProtKB | ChEBI)
Binding site669Zn2+ (UniProtKB | ChEBI)
Binding site672Zn2+ (UniProtKB | ChEBI)
Binding site692Zn2+ (UniProtKB | ChEBI)
Binding site695Zn2+ (UniProtKB | ChEBI)

GO annotations

AspectTerm
Cellular Componentchromosome
Cellular Componentnucleolus
Cellular Componentnucleoplasm
Cellular Componentnucleus
Cellular ComponentPcG protein complex
Molecular Functionhistone demethylase activity
Molecular Functionhistone H3K36 demethylase activity
Molecular Functionhistone H3K36me/H3K36me2 demethylase activity
Molecular FunctionRNA polymerase II cis-regulatory region sequence-specific DNA binding
Molecular FunctionrRNA binding
Molecular Functiontranscription coregulator activity
Molecular Functionunmethylated CpG binding
Molecular Functionzinc ion binding
Biological Processembryonic camera-type eye morphogenesis
Biological Processforebrain development
Biological Processfourth ventricle development
Biological Processhindbrain development
Biological Processinitiation of neural tube closure
Biological Processlateral ventricle development
Biological Processmidbrain development
Biological Processmidbrain-hindbrain boundary morphogenesis
Biological Processnegative regulation of neural precursor cell proliferation
Biological Processnegative regulation of neuron apoptotic process
Biological Processnegative regulation of transcription by RNA polymerase II
Biological Processpositive regulation of cell growth
Biological Processpositive regulation of stem cell population maintenance
Biological Processregulation of transcription by RNA polymerase II
Biological Processspermatogenesis
Biological Processthird ventricle development

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Lysine-specific demethylase 2B
  • EC number
  • Alternative names
    • 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 names

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

Organism names

  • Taxonomic identifier
  • Strain
    • C57BL/6J
  • Taxonomic lineage
    Eukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus

Accessions

  • Primary accession
    Q6P1G2
  • Secondary accessions
    • Q3V396
    • Q6PFD0
    • Q6ZPE8
    • Q9CSF7
    • Q9QZN6

Proteomes

Organism-specific databases

Subcellular Location

Keywords

PTM/Processing

Features

Showing features for chain, modified residue, cross-link.

TypeIDPosition(s)Description
ChainPRO_00001198541-1309Lysine-specific demethylase 2B
Modified residue26Phosphoserine
Modified residue447Phosphoserine
Modified residue450Phosphoserine
Modified residue466Phosphothreonine
Modified residue470Phosphoserine
Cross-link830Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross-link863Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Modified residue924Phosphoserine
Modified residue948Phosphoserine
Modified residue952Phosphoserine
Modified residue991Phosphoserine
Modified residue1004Phosphoserine

Keywords

Proteomic databases

PTM databases

Expression

Gene expression databases

Interaction

Subunit

Interacts with SKP1, forming heterodimers (By similarity).
The KDM2B-SKP1 heterodimeric complex interacts with the PCGF1-BCORL heterodimeric complex to form a homotetrameric polycomb repression complex 1 (PRC1.1) (By similarity).
Directly interacts with CUL1. The SKP1-KDM2B interacts with UBB (By similarity).

Binary interactions

TypeEntry 1Entry 2Number of experimentsIntact
BINARY Q6P1G2Rnf2 Q9CQJ44EBI-1216214, EBI-927321

Protein-protein interaction databases

Miscellaneous

Structure

Family & Domains

Features

Showing features for domain, compositional bias, region, zinc finger, coiled coil, repeat.

TypeIDPosition(s)Description
Domain147-315JmjC
Compositional bias378-402Acidic residues
Region378-476Disordered
Compositional bias451-476Polar residues
Zinc finger579-625CXXC-type
Zinc finger632-698PHD-type
Region700-816Disordered
Compositional bias724-787Basic and acidic residues
Compositional bias788-816Polar residues
Region828-1005Disordered
Compositional bias841-879Basic and acidic residues
Compositional bias915-936Basic and acidic residues
Coiled coil916-944
Compositional bias946-976Basic and acidic residues
Domain1032-1078F-box
Repeat1106-1127LRR 1
Repeat1129-1155LRR 2
Repeat1195-1220LRR 3
Repeat1221-1250LRR 4
Repeat1251-1275LRR 5
Repeat1276-1309LRR 6

Domain

The LRR repeats are required for the interaction with the PCGF1-BCORL1 heterodimeric complex.
The JmjC domain mediates demethylation activity (By similarity).
It is also required for repression of ribosomal RNA genes (By similarity).
The CXXC zinc finger mediates binding to DNA containing unmethylated cytidine-phosphate-guanosine (CpG) dinucleotides.
The F-box domain mediates interaction with UBB.

Sequence similarities

Belongs to the JHDM1 histone demethylase family.

Keywords

Phylogenomic databases

Family and domain databases

Sequence & Isoforms

Align isoforms (4)
  • Sequence status
    Complete

This entry describes 4 isoforms produced by Alternative splicing.

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.

  • Length
    1,309
  • Mass (Da)
    149,733
  • Last updated
    2004-07-05 v1
  • Checksum
    5BD203C3535C4D88
MEAEKDSGRRLRAIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLVFRDKDGLGIKMPDPDFTVRDVKLLVGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSHTKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNALAEMKYPKVKKYCLMSVKGCFTDFHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIELKQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIEDRTRVQPKFRYPFYYEMCWYVLERYVYCVTQRSYLTQEYQRELMLIDAPRKTSVDGFSSDSWLDMEEESCEQQPQEEEEEEEDKEEEGDGADKTPKPPTDDPTSPTSTPPEDQDSTGKKPKAPAIRFLKRTLSNESEESVKSTSMPTDDPKTPTGSPATEVSTKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIEDPQALLEGVKNVLKEHVDDDPTLAITGVPVVSWPKKTAKNRVVGRPKGKLGPASAVKLAANRTTAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCNHAGKTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSSLSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAEDRLSLANKPLRRFKQEPEDDLPEAPPKTRESDQSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLVNKELSKELSKELNHEIQKTESTLAHESQQPIKSEPESENDEPKRPLSHCERPHRFSKGLNGTPRELRHSLGPGLRSPPRVMSRPPPSASPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYLSHRDLCVCMRVCRTWNRWCCDKRLWTRIDLNRCKSITPLMLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLAGLDITDVSLRLIIRHMPLLSKLQLSYCNHINDQSINLLTAVGTTTRDSLTEVNLSDCNKVTDLCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS

Q6P1G2-2

  • Name
    2
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 1-533: Missing
    • 534-551: TLAITGVPVVSWPKKTAK → MAMSVSAEDDDYESEPDQ

Q6P1G2-3

  • Name
    3
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical
    • 627-656: PVLPHTAVCLVCGEAGKEDTVEEEEGKFNL → VSAQKAQAGLMQGLPAICPALGLLCGMGEV
    • 657-1309: Missing

Q6P1G2-4

  • Name
    4
  • See also
    sequence in UniParc or sequence clusters in UniRef
  • Differences from canonical

Computationally mapped potential isoform sequences

There are 7 potential isoforms mapped to this entry

View all
EntryEntry nameGene nameLength
F6QTG9F6QTG9_MOUSEKdm2b296
D3YV31D3YV31_MOUSEKdm2b286
D3YUE3D3YUE3_MOUSEKdm2b514
D3YVU4D3YVU4_MOUSEKdm2b1266
D3YVU7D3YVU7_MOUSEKdm2b1254
D6RHM8D6RHM8_MOUSEKdm2b38
E9QL25E9QL25_MOUSEKdm2b1303

Features

Showing features for alternative sequence, compositional bias, sequence conflict.

TypeIDPosition(s)Description
Alternative sequenceVSP_0113421-533in isoform 2
Alternative sequenceVSP_0190032-1196in isoform 4
Compositional bias378-402Acidic residues
Compositional bias451-476Polar residues
Sequence conflict461in Ref. 3; BAC98289
Alternative sequenceVSP_011343534-551in isoform 2
Alternative sequenceVSP_017477627-656in isoform 3
Alternative sequenceVSP_017478657-1309in isoform 3
Compositional bias724-787Basic and acidic residues
Compositional bias788-816Polar residues
Compositional bias841-879Basic and acidic residues
Compositional bias915-936Basic and acidic residues
Compositional bias946-976Basic and acidic residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
AK012952
EMBL· GenBank· DDBJ
BAB28568.2
EMBL· GenBank· DDBJ
mRNA
AK043352
EMBL· GenBank· DDBJ
BAE20639.1
EMBL· GenBank· DDBJ
mRNA
BC057622
EMBL· GenBank· DDBJ
AAH57622.1
EMBL· GenBank· DDBJ
mRNA
BC065090
EMBL· GenBank· DDBJ
AAH65090.1
EMBL· GenBank· DDBJ
mRNA
AK129479
EMBL· GenBank· DDBJ
BAC98289.1
EMBL· GenBank· DDBJ
mRNA
AF176524
EMBL· GenBank· DDBJ
AAF09133.1
EMBL· GenBank· DDBJ
mRNA

Genome annotation databases

Similar Proteins

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