Q6P1G2 · KDM2B_MOUSE
- ProteinLysine-specific demethylase 2B
- GeneKdm2b
- StatusUniProtKB reviewed (Swiss-Prot)
- Organism
- Amino acids1309 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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
- 2 2-oxoglutarate + N6,N6-dimethyl-L-lysyl36-[histone H3] + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl36-[histone H3] + 2 succinate
2 CHEBI:16810 + RHEA-COMP:9787 CHEBI:61976 Position: 36+ 2 CHEBI:15379 = 2 CHEBI:16526 + 2 CHEBI:16842 + RHEA-COMP:9785 CHEBI:29969 Position: 36+ 2 CHEBI:30031
Cofactor
Note: Binds 1 Fe2+ ion per subunit.
Activity regulation
Histone demethylase activity is inhibited by fumarate.
Features
Showing features for binding site.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 208 | substrate | ||||
Sequence: T | ||||||
Binding site | 211 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 213 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 228 | substrate | ||||
Sequence: K | ||||||
Binding site | 283 | Fe cation (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 586 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 589 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 592 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 597 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 600 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 603 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 619 | Zn2+ 2 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 624 | Zn2+ 1 (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 635 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 638 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 661 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 664 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 669 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: H | ||||||
Binding site | 672 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 692 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C | ||||||
Binding site | 695 | Zn2+ (UniProtKB | ChEBI) | ||||
Sequence: C |
GO annotations
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameLysine-specific demethylase 2B
- EC number
- Alternative names
Gene names
Organism names
- Organism
- Strain
- Taxonomic lineageEukaryota > Metazoa > Chordata > Craniata > Vertebrata > Euteleostomi > Mammalia > Eutheria > Euarchontoglires > Glires > Rodentia > Myomorpha > Muroidea > Muridae > Murinae > Mus > Mus
Accessions
- Primary accessionQ6P1G2
- Secondary accessions
Proteomes
Organism-specific databases
Subcellular Location
PTM/Processing
Features
Showing features for chain, modified residue, cross-link.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000119854 | 1-1309 | Lysine-specific demethylase 2B | |||
Sequence: MEAEKDSGRRLRAIDRQRYDENEDLSDVEEIVSVRGFSLEEKLRSQLYQGDFVHAMEGKDFNYEYVQREALRVPLVFRDKDGLGIKMPDPDFTVRDVKLLVGSRRLVDVMDVNTQKGTEMSMSQFVRYYETPEAQRDKLYNVISLEFSHTKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNALAEMKYPKVKKYCLMSVKGCFTDFHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIELKQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIEDRTRVQPKFRYPFYYEMCWYVLERYVYCVTQRSYLTQEYQRELMLIDAPRKTSVDGFSSDSWLDMEEESCEQQPQEEEEEEEDKEEEGDGADKTPKPPTDDPTSPTSTPPEDQDSTGKKPKAPAIRFLKRTLSNESEESVKSTSMPTDDPKTPTGSPATEVSTKWTHLTEFELKGLKALVEKLESLPENKKCVPEGIEDPQALLEGVKNVLKEHVDDDPTLAITGVPVVSWPKKTAKNRVVGRPKGKLGPASAVKLAANRTTAGARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCIAPVLPHTAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCNHAGKTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSSLSPWWRSSLTYFQQQLKPGKEDKLFRKKRRSWKNAEDRLSLANKPLRRFKQEPEDDLPEAPPKTRESDQSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLVNKELSKELSKELNHEIQKTESTLAHESQQPIKSEPESENDEPKRPLSHCERPHRFSKGLNGTPRELRHSLGPGLRSPPRVMSRPPPSASPPKCIQMERHVIRPPPISPPPDSLPLDDGAAHVMHREVWMAVFSYLSHRDLCVCMRVCRTWNRWCCDKRLWTRIDLNRCKSITPLMLSGIIRRQPVSLDLSWTNISKKQLSWLINRLPGLRDLVLSGCSWIAVSALCSSSCPLLRTLDVQWVEGLKDAQMRDLLSPPTDNRPGQMDNRSKLRNIVELRLAGLDITDVSLRLIIRHMPLLSKLQLSYCNHINDQSINLLTAVGTTTRDSLTEVNLSDCNKVTDLCLSFFKRCGNICHIDLRYCKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS | ||||||
Modified residue | 26 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 447 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 450 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 466 | Phosphothreonine | ||||
Sequence: T | ||||||
Modified residue | 470 | Phosphoserine | ||||
Sequence: S | ||||||
Cross-link | 830 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Cross-link | 863 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) | ||||
Sequence: K | ||||||
Modified residue | 924 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 948 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 952 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 991 | Phosphoserine | ||||
Sequence: S | ||||||
Modified residue | 1004 | Phosphoserine | ||||
Sequence: S |
Keywords
- PTM
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).
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
Type | Entry 1 | Entry 2 | Number of experiments | Intact | |
---|---|---|---|---|---|
BINARY | Q6P1G2 | Rnf2 Q9CQJ4 | 4 | EBI-1216214, EBI-927321 |
Protein-protein interaction databases
Miscellaneous
Structure
Family & Domains
Features
Showing features for domain, compositional bias, region, zinc finger, coiled coil, repeat.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Domain | 147-315 | JmjC | ||||
Sequence: FSHTKLEHLVKRPTVVDLVDWVDNMWPQHLKEKQTEATNALAEMKYPKVKKYCLMSVKGCFTDFHIDFGGTSVWYHVFRGGKIFWLIPPTLHNLALYEEWVLSGKQSDIFLGDRVERCQRIELKQGYTFFIPSGWIHAVYTPVDSLVFGGNILHSFNVPMQLRIYEIED | ||||||
Compositional bias | 378-402 | Acidic residues | ||||
Sequence: DMEEESCEQQPQEEEEEEEDKEEEG | ||||||
Region | 378-476 | Disordered | ||||
Sequence: DMEEESCEQQPQEEEEEEEDKEEEGDGADKTPKPPTDDPTSPTSTPPEDQDSTGKKPKAPAIRFLKRTLSNESEESVKSTSMPTDDPKTPTGSPATEVS | ||||||
Compositional bias | 451-476 | Polar residues | ||||
Sequence: EESVKSTSMPTDDPKTPTGSPATEVS | ||||||
Zinc finger | 579-625 | CXXC-type | ||||
Sequence: ARRRRTRCRKCEACLRTECGECHFCKDMKKFGGPGRMKQSCIMRQCI | ||||||
Zinc finger | 632-698 | PHD-type | ||||
Sequence: TAVCLVCGEAGKEDTVEEEEGKFNLMLMECSICNEIIHPGCLKIKESEGVVNDELPNCWECPKCNHA | ||||||
Region | 700-816 | Disordered | ||||
Sequence: KTGKQKRGPGFKYASNLPGSLLKEQKMNRDNKEGQEPAKRRSECEEAPRRRSDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSGRKRASSLQTSPGSSSHLSPRPPLGSSLSP | ||||||
Compositional bias | 724-787 | Basic and acidic residues | ||||
Sequence: QKMNRDNKEGQEPAKRRSECEEAPRRRSDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSG | ||||||
Compositional bias | 788-816 | Polar residues | ||||
Sequence: RKRASSLQTSPGSSSHLSPRPPLGSSLSP | ||||||
Region | 828-1005 | Disordered | ||||
Sequence: QLKPGKEDKLFRKKRRSWKNAEDRLSLANKPLRRFKQEPEDDLPEAPPKTRESDQSRSSSPTAGPSTEGAEGPEEKKKVKMRRKRRLVNKELSKELSKELNHEIQKTESTLAHESQQPIKSEPESENDEPKRPLSHCERPHRFSKGLNGTPRELRHSLGPGLRSPPRVMSRPPPSASP | ||||||
Compositional bias | 841-879 | Basic and acidic residues | ||||
Sequence: KRRSWKNAEDRLSLANKPLRRFKQEPEDDLPEAPPKTRE | ||||||
Compositional bias | 915-936 | Basic and acidic residues | ||||
Sequence: VNKELSKELSKELNHEIQKTES | ||||||
Coiled coil | 916-944 | |||||
Sequence: NKELSKELSKELNHEIQKTESTLAHESQQ | ||||||
Compositional bias | 946-976 | Basic and acidic residues | ||||
Sequence: IKSEPESENDEPKRPLSHCERPHRFSKGLNG | ||||||
Domain | 1032-1078 | F-box | ||||
Sequence: DGAAHVMHREVWMAVFSYLSHRDLCVCMRVCRTWNRWCCDKRLWTRI | ||||||
Repeat | 1106-1127 | LRR 1 | ||||
Sequence: WTNISKKQLSWLINRLPGLRDL | ||||||
Repeat | 1129-1155 | LRR 2 | ||||
Sequence: LSGCSWIAVSALCSSSCPLLRTLDVQW | ||||||
Repeat | 1195-1220 | LRR 3 | ||||
Sequence: GLDITDVSLRLIIRHMPLLSKLQLSY | ||||||
Repeat | 1221-1250 | LRR 4 | ||||
Sequence: CNHINDQSINLLTAVGTTTRDSLTEVNLSD | ||||||
Repeat | 1251-1275 | LRR 5 | ||||
Sequence: CNKVTDLCLSFFKRCGNICHIDLRY | ||||||
Repeat | 1276-1309 | LRR 6 | ||||
Sequence: CKQVTKEGCEQFIAEMSVSVQFGQVEEKLLQKLS |
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).
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
- Domain
Phylogenomic databases
Family and domain databases
Sequence & Isoforms
- Sequence statusComplete
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.
- Name1
- Length1,309
- Mass (Da)149,733
- Last updated2004-07-05 v1
- Checksum5BD203C3535C4D88
Q6P1G2-2
- Name2
Q6P1G2-3
- Name3
Q6P1G2-4
- Name4
- Differences from canonical
- 2-1196: Missing
Computationally mapped potential isoform sequences
There are 7 potential isoforms mapped to this entry
Features
Showing features for alternative sequence, compositional bias, sequence conflict.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Alternative sequence | VSP_011342 | 1-533 | in isoform 2 | |||
Sequence: Missing | ||||||
Alternative sequence | VSP_019003 | 2-1196 | in isoform 4 | |||
Sequence: Missing | ||||||
Compositional bias | 378-402 | Acidic residues | ||||
Sequence: DMEEESCEQQPQEEEEEEEDKEEEG | ||||||
Compositional bias | 451-476 | Polar residues | ||||
Sequence: EESVKSTSMPTDDPKTPTGSPATEVS | ||||||
Sequence conflict | 461 | in Ref. 3; BAC98289 | ||||
Sequence: T → M | ||||||
Alternative sequence | VSP_011343 | 534-551 | in isoform 2 | |||
Sequence: TLAITGVPVVSWPKKTAK → MAMSVSAEDDDYESEPDQ | ||||||
Alternative sequence | VSP_017477 | 627-656 | in isoform 3 | |||
Sequence: PVLPHTAVCLVCGEAGKEDTVEEEEGKFNL → VSAQKAQAGLMQGLPAICPALGLLCGMGEV | ||||||
Alternative sequence | VSP_017478 | 657-1309 | in isoform 3 | |||
Sequence: Missing | ||||||
Compositional bias | 724-787 | Basic and acidic residues | ||||
Sequence: QKMNRDNKEGQEPAKRRSECEEAPRRRSDEHPKKVPADGILRRKSDDVHLRRKRKYEKPQELSG | ||||||
Compositional bias | 788-816 | Polar residues | ||||
Sequence: RKRASSLQTSPGSSSHLSPRPPLGSSLSP | ||||||
Compositional bias | 841-879 | Basic and acidic residues | ||||
Sequence: KRRSWKNAEDRLSLANKPLRRFKQEPEDDLPEAPPKTRE | ||||||
Compositional bias | 915-936 | Basic and acidic residues | ||||
Sequence: VNKELSKELSKELNHEIQKTES | ||||||
Compositional bias | 946-976 | Basic and acidic residues | ||||
Sequence: IKSEPESENDEPKRPLSHCERPHRFSKGLNG |
Keywords
- Coding sequence diversity
- Technical term
Sequence databases
Nucleotide Sequence | Protein Sequence | Molecule Type | Status | |
---|---|---|---|---|
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 |