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Protein

Lysine-specific histone demethylase 1B

Gene

KDM1B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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 H4.2 Publications

Cofactori

Protein has several cofactor binding sites:

Activity regulationi

Histone H3K4me1 and H3K4me2 demethylase activity is enhanced by GLYR1.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi53Zinc 1Combined sources3 Publications1
Metal bindingi58Zinc 1Combined sources3 Publications1
Metal bindingi65Zinc 2Combined sources3 Publications1
Metal bindingi73Zinc 2Combined sources3 Publications1
Metal bindingi84Zinc 1; via pros nitrogenCombined sources3 Publications1
Metal bindingi90Zinc 1; via tele nitrogenCombined sources3 Publications1
Metal bindingi92Zinc 2Combined sources3 Publications1
Metal bindingi95Zinc 2Combined sources3 Publications1
Metal bindingi142Zinc 3Combined sources3 Publications1
Metal bindingi147Zinc 3Combined sources3 Publications1
Metal bindingi169Zinc 3Combined sources3 Publications1
Metal bindingi185Zinc 3Combined sources3 Publications1
Binding sitei598FAD; via amide nitrogen and carbonyl oxygenCombined sources3 Publications1
Binding sitei795FAD; via amide nitrogenCombined sources2 Publications1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri133 – 193CW-typePROSITE-ProRule annotationAdd BLAST61
Nucleotide bindingi383 – 439FADSequence analysisCombined sources3 PublicationsAdd BLAST57
Nucleotide bindingi803 – 805FADCombined sources3 Publications3

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Developmental protein, Oxidoreductase, Repressor
Biological processTranscription, Transcription regulation
LigandFAD, Flavoprotein, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214842 HDMs demethylate histones
R-HSA-5689603 UCH proteinases

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific histone demethylase 1B (EC:1.-.-.-)
Alternative name(s):
Flavin-containing amine oxidase domain-containing protein 1
Lysine-specific histone demethylase 2
Gene namesi
Name:KDM1B
Synonyms:AOF1, C6orf193, LSD2
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000165097.13
HGNCiHGNC:21577 KDM1B
MIMi613081 gene
neXtProtiNX_Q8NB78

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

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi48 – 49KK → AA: Normal demethylase activity. 1 Publication2
Mutagenesisi51 – 52RK → AA: Reduced demethylase activity. 1 Publication2
Mutagenesisi53C → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi82W → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi84H → A: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication1
Mutagenesisi90H → A: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication1
Mutagenesisi101R → A: Reduced demethylase activity. 1 Publication1
Mutagenesisi114 – 115KK → AA: Reduced demethylase activity. 1 Publication2
Mutagenesisi139W → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi150W → A: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication1
Mutagenesisi151R → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi185C → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi273 – 278YQPNEC → GSGSGS: Strongly reduced demethylase activity. Loss of enzymatic activity; when associated with 285-A--A-287. 1 Publication6
Mutagenesisi285 – 287RPD → APA: Strongly reduced demethylase activity. Loss of enzymatic activity; when associated with 273-G--S-278. 1 Publication3
Mutagenesisi318 – 319WY → AA: Loss of demethylase activity. 1 Publication2
Mutagenesisi340 – 341LV → AA: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication2
Mutagenesisi361 – 362LI → AA: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication2
Mutagenesisi443 – 444IN → GG: Loss of demethylase activity. Defective in the binding of FAD. 1 Publication2
Mutagenesisi542N → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi543L → A: Reduced demethylase activity. 1 Publication1
Mutagenesisi547C → A: Reduced demethylase activity. 1 Publication1
Mutagenesisi559W → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi563E → A: Loss of demethylase activity. 1 Publication1
Mutagenesisi661K → A: Normal demethylase activity. 1 Publication1
Mutagenesisi767Y → A: Loss of demethylase activity. 1 Publication1

Organism-specific databases

DisGeNETi221656
OpenTargetsiENSG00000165097
PharmGKBiPA162379723
PA165617946

Chemistry databases

ChEMBLiCHEMBL1938208

Polymorphism and mutation databases

BioMutaiKDM1B
DMDMi317373434

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002473361 – 822Lysine-specific histone demethylase 1BAdd BLAST822

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei13PhosphoserineCombined sources1
Modified residuei17PhosphoserineCombined sources1
Modified residuei26PhosphoserineCombined sources1
Modified residuei247PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ8NB78
MaxQBiQ8NB78
PaxDbiQ8NB78
PeptideAtlasiQ8NB78
PRIDEiQ8NB78
ProteomicsDBi72745
72746 [Q8NB78-2]
72747 [Q8NB78-4]

PTM databases

iPTMnetiQ8NB78
PhosphoSitePlusiQ8NB78

Expressioni

Gene expression databases

BgeeiENSG00000165097 Expressed in 189 organ(s), highest expression level in secondary oocyte
CleanExiHS_AOF1
ExpressionAtlasiQ8NB78 baseline and differential
GenevisibleiQ8NB78 HS

Organism-specific databases

HPAiHPA031269

Interactioni

Subunit structurei

Does not form a complex with RCOR1/CoREST (By similarity). Interacts with its cofactor GLYR1 at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation (PubMed:23260659).By similarity1 Publication

GO - Molecular functioni

Protein-protein interaction databases

BioGridi128743, 30 interactors
IntActiQ8NB78, 14 interactors
STRINGi9606.ENSP00000297792

Chemistry databases

BindingDBiQ8NB78

Structurei

Secondary structure

1822
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ8NB78
SMRiQ8NB78
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini275 – 373SWIRMPROSITE-ProRule annotationAdd BLAST99

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni273 – 292GLYR1-bindingCombined sources1 PublicationAdd BLAST20
Regioni438 – 467Histone H3-bindingCombined sources2 PublicationsAdd BLAST30
Regioni487 – 498Histone H3-bindingCombined sources2 PublicationsAdd BLAST12
Regioni538 – 572Histone H3-bindingCombined sources2 PublicationsAdd BLAST35
Regioni564 – 566GLYR1-bindingCombined sources1 Publication3
Regioni798 – 814GLYR1-bindingCombined sources1 PublicationAdd BLAST17

Domaini

The SWIRM domain may act as an anchor site for a histone tail.By similarity

Sequence similaritiesi

Belongs to the flavin monoamine oxidase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri133 – 193CW-typePROSITE-ProRule annotationAdd BLAST61

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG0029 Eukaryota
ENOG410XSNC LUCA
GeneTreeiENSGT00530000062888
HOGENOMiHOG000230870
HOVERGENiHBG079963
InParanoidiQ8NB78
KOiK19413
PhylomeDBiQ8NB78
TreeFamiTF352593

Family and domain databases

Gene3Di1.10.10.10, 1 hit
3.50.50.60, 1 hit
InterProiView protein in InterPro
IPR002937 Amino_oxidase
IPR036188 FAD/NAD-bd_sf
IPR009057 Homeobox-like_sf
IPR007526 SWIRM
IPR036388 WH-like_DNA-bd_sf
IPR011124 Znf_CW
PfamiView protein in Pfam
PF01593 Amino_oxidase, 1 hit
PF04433 SWIRM, 1 hit
PF07496 zf-CW, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
SSF51905 SSF51905, 1 hit
PROSITEiView protein in PROSITE
PS50934 SWIRM, 1 hit
PS51050 ZF_CW, 1 hit

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 2 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q8NB78-1) [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
MATPRGRTKK KASFDHSPDS LPLRSSGRQA KKKATETTDE DEDGGSEKKY
60 70 80 90 100
RKCEKAGCTA TCPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY
110 120 130 140 150
RSHKDGYDKY TTWKKIWTSN GKTEPSPKAF MADQQLPYWV QCTKPECRKW
160 170 180 190 200
RQLTKEIQLT PQIAKTYRCG MKPNTAIKPE TSDHCSLPED LRVLEVSNHW
210 220 230 240 250
WYSMLILPPL LKDSVAAPLL SAYYPDCVGM SPSCTSTNRA AATGNASPGK
260 270 280 290 300
LEHSKAALSV HVPGMNRYFQ PFYQPNECGK ALCVRPDVME LDELYEFPEY
310 320 330 340 350
SRDPTMYLAL RNLILALWYT NCKEALTPQK CIPHIIVRGL VRIRCVQEVE
360 370 380 390 400
RILYFMTRKG LINTGVLSVG ADQYLLPKDY HNKSVIIIGA GPAGLAAARQ
410 420 430 440 450
LHNFGIKVTV LEAKDRIGGR VWDDKSFKGV TVGRGAQIVN GCINNPVALM
460 470 480 490 500
CEQLGISMHK FGERCDLIQE GGRITDPTID KRMDFHFNAL LDVVSEWRKD
510 520 530 540 550
KTQLQDVPLG EKIEEIYKAF IKESGIQFSE LEGQVLQFHL SNLEYACGSN
560 570 580 590 600
LHQVSARSWD HNEFFAQFAG DHTLLTPGYS VIIEKLAEGL DIQLKSPVQC
610 620 630 640 650
IDYSGDEVQV TTTDGTGYSA QKVLVTVPLA LLQKGAIQFN PPLSEKKMKA
660 670 680 690 700
INSLGAGIIE KIALQFPYRF WDSKVQGADF FGHVPPSASK RGLFAVFYDM
710 720 730 740 750
DPQKKHSVLM SVIAGEAVAS VRTLDDKQVL QQCMATLREL FKEQEVPDPT
760 770 780 790 800
KYFVTRWSTD PWIQMAYSFV KTGGSGEAYD IIAEDIQGTV FFAGEATNRH
810 820
FPQTVTGAYL SGVREASKIA AF
Length:822
Mass (Da):92,098
Last modified:January 11, 2011 - v3
Checksum:i6C0A9BD6B2CEA2EA
GO
Isoform 2 (identifier: Q8NB78-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     192-323: Missing.
     453-552: Missing.

Note: No experimental confirmation available.
Show »
Length:590
Mass (Da):65,717
Checksum:iAFDC638DFD727A9E
GO
Isoform 4 (identifier: Q8NB78-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-647: Missing.

Note: No experimental confirmation available.
Show »
Length:175
Mass (Da):19,428
Checksum:i5571123B00CDE9E8
GO

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y6H0H0Y6H0_HUMAN
Lysine-specific histone demethylase...
KDM1B
823Annotation score:
Q08EI0Q08EI0_HUMAN
AOF1 protein
KDM1B AOF1
113Annotation score:

Sequence cautioni

The sequence BAC03663 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti651I → T in BAC86124 (PubMed:14702039).Curated1
Sequence conflicti794 – 795Missing in CAH10499 (PubMed:17974005).Curated2

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0199631 – 647Missing in isoform 4. 1 PublicationAdd BLAST647
Alternative sequenceiVSP_019964192 – 323Missing in isoform 2. 1 PublicationAdd BLAST132
Alternative sequenceiVSP_019965453 – 552Missing in isoform 2. 1 PublicationAdd BLAST100

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK091217 mRNA Translation: BAC03612.1
AK091428 mRNA Translation: BAC03663.1 Different initiation.
AK125318 mRNA Translation: BAC86124.1
AL031774 Genomic DNA No translation available.
AL589723 Genomic DNA No translation available.
CH471087 Genomic DNA Translation: EAW55401.1
CR627410 mRNA Translation: CAH10499.1
CCDSiCCDS34343.1 [Q8NB78-2]
RefSeqiNP_694587.3, NM_153042.3 [Q8NB78-2]
XP_005248983.1, XM_005248926.1 [Q8NB78-1]
UniGeneiHs.709336

Genome annotation databases

EnsembliENST00000297792; ENSP00000297792; ENSG00000165097 [Q8NB78-2]
GeneIDi221656
KEGGihsa:221656
UCSCiuc003ncn.2 human [Q8NB78-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK091217 mRNA Translation: BAC03612.1
AK091428 mRNA Translation: BAC03663.1 Different initiation.
AK125318 mRNA Translation: BAC86124.1
AL031774 Genomic DNA No translation available.
AL589723 Genomic DNA No translation available.
CH471087 Genomic DNA Translation: EAW55401.1
CR627410 mRNA Translation: CAH10499.1
CCDSiCCDS34343.1 [Q8NB78-2]
RefSeqiNP_694587.3, NM_153042.3 [Q8NB78-2]
XP_005248983.1, XM_005248926.1 [Q8NB78-1]
UniGeneiHs.709336

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4FWEX-ray2.13A30-822[»]
4FWFX-ray2.70A30-822[»]
4FWJX-ray2.90A/B30-822[»]
4GU0X-ray3.10A/B/C/D51-822[»]
4GU1X-ray2.94A/B51-822[»]
4GURX-ray2.51A51-822[»]
4GUSX-ray2.23A51-822[»]
4GUTX-ray2.00A51-822[»]
4GUUX-ray2.30A51-822[»]
4HSUX-ray1.99A51-822[»]
ProteinModelPortaliQ8NB78
SMRiQ8NB78
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi128743, 30 interactors
IntActiQ8NB78, 14 interactors
STRINGi9606.ENSP00000297792

Chemistry databases

BindingDBiQ8NB78
ChEMBLiCHEMBL1938208

PTM databases

iPTMnetiQ8NB78
PhosphoSitePlusiQ8NB78

Polymorphism and mutation databases

BioMutaiKDM1B
DMDMi317373434

Proteomic databases

EPDiQ8NB78
MaxQBiQ8NB78
PaxDbiQ8NB78
PeptideAtlasiQ8NB78
PRIDEiQ8NB78
ProteomicsDBi72745
72746 [Q8NB78-2]
72747 [Q8NB78-4]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000297792; ENSP00000297792; ENSG00000165097 [Q8NB78-2]
GeneIDi221656
KEGGihsa:221656
UCSCiuc003ncn.2 human [Q8NB78-1]

Organism-specific databases

CTDi221656
DisGeNETi221656
EuPathDBiHostDB:ENSG00000165097.13
GeneCardsiKDM1B
H-InvDBiHIX0005608
HGNCiHGNC:21577 KDM1B
HPAiHPA031269
MIMi613081 gene
neXtProtiNX_Q8NB78
OpenTargetsiENSG00000165097
PharmGKBiPA162379723
PA165617946
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0029 Eukaryota
ENOG410XSNC LUCA
GeneTreeiENSGT00530000062888
HOGENOMiHOG000230870
HOVERGENiHBG079963
InParanoidiQ8NB78
KOiK19413
PhylomeDBiQ8NB78
TreeFamiTF352593

Enzyme and pathway databases

ReactomeiR-HSA-3214842 HDMs demethylate histones
R-HSA-5689603 UCH proteinases

Miscellaneous databases

ChiTaRSiKDM1B human
GenomeRNAii221656
PROiPR:Q8NB78
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165097 Expressed in 189 organ(s), highest expression level in secondary oocyte
CleanExiHS_AOF1
ExpressionAtlasiQ8NB78 baseline and differential
GenevisibleiQ8NB78 HS

Family and domain databases

Gene3Di1.10.10.10, 1 hit
3.50.50.60, 1 hit
InterProiView protein in InterPro
IPR002937 Amino_oxidase
IPR036188 FAD/NAD-bd_sf
IPR009057 Homeobox-like_sf
IPR007526 SWIRM
IPR036388 WH-like_DNA-bd_sf
IPR011124 Znf_CW
PfamiView protein in Pfam
PF01593 Amino_oxidase, 1 hit
PF04433 SWIRM, 1 hit
PF07496 zf-CW, 1 hit
SUPFAMiSSF46689 SSF46689, 1 hit
SSF51905 SSF51905, 1 hit
PROSITEiView protein in PROSITE
PS50934 SWIRM, 1 hit
PS51050 ZF_CW, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiKDM1B_HUMAN
AccessioniPrimary (citable) accession number: Q8NB78
Secondary accession number(s): A2A2C5
, A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q96EL7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 25, 2006
Last sequence update: January 11, 2011
Last modified: November 7, 2018
This is version 139 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
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