Reactome | UniProt:Q8NB78 KDM1B

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UniProt:Q8NB78 KDM1B Show undefined attributes

chain	chain:1-822
checksum	6C0A9BD6B2CEA2EA
comment	FUNCTION Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of GLYR1 to achieve such activity, they form a multifunctional enzyme complex that modifies transcribed chromatin and facilitates Pol II transcription through nucleosomes (PubMed:30970244).CATALYTIC ACTIVITY N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] + 2 A + 2 H2O = L-lysyl(4)-[histone H3] + 2 formaldehyde + 2 AH2CATALYTIC ACTIVITY N(6)-methyl-L-lysyl(4)-[histone H3] + A + H2O = L-lysyl(4)-[histone H3] + formaldehyde + AH2COFACTOR Binds 3 Zn(2+) ions per subunit.ACTIVITY REGULATION Histone H3K4me1 and H3K4me2 demethylase activity is inhibited by DNA, this inhibition is released in complex with GLYR1.BIOPHYSICOCHEMICAL PROPERTIES Kcat is 0.56 min(-1) for N(6)-methyl-L-lysyl(4)-[histone H3] and 1.30 min(-1) for N(6),N(6)-dimethyl-L-lysyl(4)-[histone H3] as substrates.SUBUNIT Interacts with its cofactor GLYR1 at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation (PubMed:23260659, PubMed:30970244). In contrast to KDM1A, does not form a complex with RCOR1/CoREST (Probable). Possible accessory component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of BAP1, one of ASXL1, ASXL2 or (probably) ASXL3 and one of MBD5 or MBD6 (PubMed:30664650). The PR-DUB core associates with a number of accessory proteins, including FOXK1, FOXK2, KDM1B, HCFC1 and OGT; KDM1B specifically associates with ASXL2 PR-DUB complexes (PubMed:30664650).INTERACTION Found in actively RNAPolII-transcribed gene bodies.ALTERNATIVE PRODUCTS Belongs to the flavin monoamine oxidase family.SEQUENCE CAUTION Truncated N-terminus.
created	[InstanceEdit:217385] Schmidt, EE, 2008-03-27 06:23:53
crossReference	[DatabaseIdentifier:11471985] ENSEMBL:ENSG00000165097 [DatabaseIdentifier:12815828] ZINC target:Q8NB78 [DatabaseIdentifier:12812461] ZINC - Substances:KDM1B_HUMAN [DatabaseIdentifier:11569406] ENSEMBL:ENSP00000499208 [DatabaseIdentifier:11569407] ENSEMBL:ENSP00000297792 [DatabaseIdentifier:11692105] ENSEMBL:ENST00000650836 [DatabaseIdentifier:11692106] ENSEMBL:ENST00000297792 [DatabaseIdentifier:11781198] Guide to Pharmacology - Targets:2670 [DatabaseIdentifier:11787494] GeneCards:KDM1B [DatabaseIdentifier:11802932] GlyGen:Q8NB78 [DatabaseIdentifier:11831667] HMDB Protein:HMDBP08264 [DatabaseIdentifier:11840565] HPA:ENSG00000165097-KDM1B [DatabaseIdentifier:12125106] OpenTargets:ENSG00000165097 [DatabaseIdentifier:12177315] PDB:4GUS [DatabaseIdentifier:12177316] PDB:4GUT [DatabaseIdentifier:12177314] PDB:4GUR [DatabaseIdentifier:12165935] PDB:6R25 [DatabaseIdentifier:12177321] PDB:4GU0 [DatabaseIdentifier:12177318] PDB:4HSU [DatabaseIdentifier:12177322] PDB:4GU1 [DatabaseIdentifier:12177319] PDB:7XE2 [DatabaseIdentifier:12177320] PDB:7XE3 [DatabaseIdentifier:12177317] PDB:4GUU [DatabaseIdentifier:12165963] PDB:6R1U [DatabaseIdentifier:12177326] PDB:4FWJ [DatabaseIdentifier:12177324] PDB:4FWE [DatabaseIdentifier:12177323] PDB:7XE1 [DatabaseIdentifier:12177325] PDB:4FWF [DatabaseIdentifier:12264508] PRO:Q8NB78 [DatabaseIdentifier:12285414] Pharos - Targets:Q8NB78 [DatabaseIdentifier:12367473] RefSeq:NP_001426059.1 [DatabaseIdentifier:12367472] RefSeq:NP_001351543.1 [DatabaseIdentifier:12367474] RefSeq:NP_694587.3
databaseName	UniProt
dbId	218809
description	recommendedName: fullName evidence="12"Lysine-specific histone demethylase 2 ecNumber evidence="5 7 9"1.14.99.66 alternativeName: Flavin-containing amine oxidase domain-containing protein 1 alternativeName: fullName evidence="12"Lysine-specific histone demethylase 1B
displayName	UniProt:Q8NB78 KDM1B
geneName	KDM1B AOF1 C6orf193 LSD2
identifier	Q8NB78
isSequenceChanged	false
keyword	3D-structure Alternative splicing Chromatin regulator Chromosome Developmental protein FAD Flavoprotein Metal-binding Nucleus Oxidoreductase Phosphoprotein Proteomics identification Reference proteome Repressor Transcription Transcription regulation Zinc Zinc-finger
modified	[InstanceEdit:9939033] Weiser, Joel, 2025-02-21
moleculeType	Protein
name	KDM1B
otherIdentifier	11719912_a_at 11751862_a_at 1553150_PM_at 1553150_at 17005169 221656 227021_PM_at 227021_at 2897110 2897112 2897113 2897115 2897117 2897118 2897120 2897122 2897125 2897127 2897128 2897129 2897130 2897131 2897132 2897134 2897135 2897137 2897139 2897140 2897142 2897143 2897144 2897145 2897146 2897148 2897150 2897151 2897152 2897153 2897154 2897155 2897156 2897157 2897158 2897159 61273_s_at 62487_i_at 77891_at 8117081 A_14_P110238 A_14_P112699 A_14_P133581 A_23_P338401 GE88023 GO:0000786 GO:0003824 GO:0005515 GO:0005634 GO:0005654 GO:0005694 GO:0006325 GO:0008270 GO:0016491 GO:0032452 GO:0032453 GO:0040029 GO:0042393 GO:0044726 GO:0046872 GO:0050660 GO:0071514 GO:0071949 GO:0140096 GO:0140682 HMNXSV003002105 HMNXSV003008121 Hs.237691.0.A1_3p_at ILMN_1781537 PH_hs_0012866 TC06000117.hg
physicalEntity	[EntityWithAccessionedSequence:R-HSA-5423072] KDM1B [nucleoplasm] - Homo sapiens
referenceDatabase	[ReferenceDatabase:2] UniProt
referenceGene	[ReferenceDNASequence:ensembl:ENSG00000165097] ENSEMBL:ENSG00000165097 KDM1B [ReferenceDNASequence:12738122] UCSC:Q8NB78 KDM1B [ReferenceDNASequence:11337055] BioGPS Gene:221656 KDM1B [ReferenceDNASequence:11399309] COSMIC - genes:KDM1B KDM1B [ReferenceDNASequence:11413252] CTD Gene:221656 KDM1B [ReferenceDNASequence:11436299] dbSNP Gene:221656 KDM1B [ReferenceDNASequence:11819135] HGNC:21577 KDM1B [ReferenceDNASequence:11878096] KEGG:hsa:221656 KDM1B [ReferenceDNASequence:11966844] Monarch:221656 KDM1B [ReferenceDNASequence:12050937] NCBI Gene:221656 KDM1B [ReferenceDNASequence:12110451] OMIM:613081 KDM1B
referenceTranscript	[ReferenceRNASequence:12549314] RefSeq:NM_001439130.1 KDM1B [ReferenceRNASequence:12549313] RefSeq:NM_153042.3 KDM1B [ReferenceRNASequence:12549315] RefSeq:NM_001364614.2 KDM1B
schemaClass	ReferenceGeneProduct
secondaryIdentifier	KDM1B_HUMAN A2A2C5 A2A2C6 Q5TGV3 Q6AI15 Q6ZUU4 Q8N258 Q96EL7
sequenceLength	822
species	[Species:48887] Homo sapiens
stId	uniprot:Q8NB78
url	http://purl.uniprot.org/uniprot/Q8NB78

Referrals

(referenceEntity)	[EntityWithAccessionedSequence:R-HSA-5423072] KDM1B [nucleoplasm]
(interactor)	[UndirectedInteraction:11204551] UniProt:Q8TDQ0 <-> UniProt:Q8NB78 (IntAct) [UndirectedInteraction:11289135] UniProt:Q92560 <-> UniProt:Q8NB78 (IntAct)