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Protein

Lysine-specific histone demethylase 1B

Gene

KDM1B

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 (By similarity).By similarity

Cofactori

FADBy similarity

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri133 – 193CW-typePROSITE-ProRule annotationAdd BLAST61
Nucleotide bindingi383 – 439FADSequence analysisAdd BLAST57

GO - Molecular functioni

GO - Biological processi

  • DNA methylation involved in gamete generation Source: Ensembl
  • histone H3-K4 demethylation Source: UniProtKB
  • multicellular organism development Source: UniProtKB-KW
  • regulation of DNA methylation Source: UniProtKB
  • regulation of gene expression by genetic imprinting Source: UniProtKB
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Oxidoreductase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

FAD, Flavoprotein, Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000165097-MONOMER.
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

HGNCiHGNC:21577. KDM1B.

Subcellular locationi

GO - Cellular componenti

  • nucleoplasm Source: Reactome
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

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.

PTM databases

iPTMnetiQ8NB78.
PhosphoSitePlusiQ8NB78.

Expressioni

Gene expression databases

BgeeiENSG00000165097.
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

Protein-protein interaction databases

BioGridi128743. 24 interactors.
IntActiQ8NB78. 12 interactors.
STRINGi9606.ENSP00000297792.

Chemistry databases

BindingDBiQ8NB78.

Structurei

Secondary structure

1822
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi51 – 55Combined sources5
Beta strandi70 – 72Combined sources3
Beta strandi75 – 77Combined sources3
Beta strandi82 – 86Combined sources5
Beta strandi89 – 92Combined sources4
Helixi93 – 100Combined sources8
Helixi104 – 106Combined sources3
Helixi107 – 116Combined sources10
Turni117 – 120Combined sources4
Helixi127 – 134Combined sources8
Beta strandi139 – 141Combined sources3
Turni145 – 147Combined sources3
Beta strandi150 – 152Combined sources3
Helixi161 – 166Combined sources6
Beta strandi173 – 175Combined sources3
Beta strandi180 – 182Combined sources3
Helixi184 – 186Combined sources3
Helixi192 – 195Combined sources4
Helixi199 – 203Combined sources5
Beta strandi211 – 213Combined sources3
Helixi217 – 219Combined sources3
Helixi225 – 227Combined sources3
Helixi267 – 269Combined sources3
Beta strandi286 – 288Combined sources3
Helixi291 – 296Combined sources6
Helixi298 – 300Combined sources3
Helixi305 – 320Combined sources16
Helixi328 – 331Combined sources4
Helixi332 – 334Combined sources3
Helixi341 – 358Combined sources18
Beta strandi361 – 363Combined sources3
Helixi371 – 373Combined sources3
Helixi378 – 380Combined sources3
Beta strandi384 – 388Combined sources5
Helixi392 – 404Combined sources13
Beta strandi407 – 411Combined sources5
Beta strandi413 – 417Combined sources5
Beta strandi427 – 430Combined sources4
Beta strandi432 – 435Combined sources4
Beta strandi438 – 440Combined sources3
Helixi446 – 454Combined sources9
Beta strandi458 – 460Combined sources3
Beta strandi467 – 469Combined sources3
Helixi477 – 497Combined sources21
Helixi498 – 500Combined sources3
Helixi503 – 505Combined sources3
Helixi509 – 523Combined sources15
Helixi530 – 547Combined sources18
Turni551 – 553Combined sources3
Turni556 – 560Combined sources5
Helixi561 – 564Combined sources4
Beta strandi572 – 574Combined sources3
Helixi580 – 587Combined sources8
Beta strandi592 – 595Combined sources4
Beta strandi598 – 602Combined sources5
Beta strandi604 – 612Combined sources9
Beta strandi617 – 625Combined sources9
Helixi629 – 634Combined sources6
Beta strandi637 – 641Combined sources5
Helixi645 – 653Combined sources9
Beta strandi654 – 657Combined sources4
Beta strandi660 – 665Combined sources6
Helixi672 – 675Combined sources4
Beta strandi679 – 683Combined sources5
Beta strandi686 – 688Combined sources3
Turni689 – 692Combined sources4
Beta strandi693 – 700Combined sources8
Beta strandi708 – 713Combined sources6
Helixi716 – 720Combined sources5
Turni721 – 723Combined sources3
Helixi726 – 740Combined sources15
Turni741 – 743Combined sources3
Beta strandi750 – 754Combined sources5
Helixi757 – 759Combined sources3
Turni761 – 763Combined sources3
Beta strandi766 – 771Combined sources6
Helixi777 – 783Combined sources7
Turni787 – 789Combined sources3
Beta strandi790 – 792Combined sources3
Helixi795 – 797Combined sources3
Beta strandi799 – 801Combined sources3
Helixi805 – 821Combined sources17

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...

Family & Domainsi

Domains and Repeats

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

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
Contains 1 CW-type zinc finger.PROSITE-ProRule annotation
Contains 1 SWIRM domain.PROSITE-ProRule annotation

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. 2 hits.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_dom.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
IPR011124. Znf_CW.
[Graphical view]
PfamiPF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
PF07496. zf-CW. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF51905. SSF51905. 2 hits.
PROSITEiPS50934. SWIRM. 1 hit.
PS51050. ZF_CW. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

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

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.
AL589723, AL031774 Genomic DNA. Translation: CAM14159.1.
AL589723, AL031774 Genomic DNA. Translation: CAM14160.1.
AL031774, AL589723 Genomic DNA. Translation: CAM28216.1.
AL031774, AL589723 Genomic DNA. Translation: CAM28217.1.
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

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.
AL589723, AL031774 Genomic DNA. Translation: CAM14159.1.
AL589723, AL031774 Genomic DNA. Translation: CAM14160.1.
AL031774, AL589723 Genomic DNA. Translation: CAM28216.1.
AL031774, AL589723 Genomic DNA. Translation: CAM28217.1.
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. 24 interactors.
IntActiQ8NB78. 12 interactors.
STRINGi9606.ENSP00000297792.

Chemistry databases

BindingDBiQ8NB78.
ChEMBLiCHEMBL1938208.

PTM databases

iPTMnetiQ8NB78.
PhosphoSitePlusiQ8NB78.

Polymorphism and mutation databases

BioMutaiKDM1B.
DMDMi317373434.

Proteomic databases

EPDiQ8NB78.
MaxQBiQ8NB78.
PaxDbiQ8NB78.
PeptideAtlasiQ8NB78.
PRIDEiQ8NB78.

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.
GeneCardsiKDM1B.
H-InvDBHIX0005608.
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

BioCyciZFISH:ENSG00000165097-MONOMER.
ReactomeiR-HSA-3214842. HDMs demethylate histones.
R-HSA-5689603. UCH proteinases.

Miscellaneous databases

ChiTaRSiKDM1B. human.
GenomeRNAii221656.
PROiQ8NB78.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000165097.
CleanExiHS_AOF1.
ExpressionAtlasiQ8NB78. baseline and differential.
GenevisibleiQ8NB78. HS.

Family and domain databases

Gene3Di1.10.10.10. 1 hit.
3.50.50.60. 2 hits.
InterProiIPR002937. Amino_oxidase.
IPR023753. FAD/NAD-binding_dom.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
IPR011124. Znf_CW.
[Graphical view]
PfamiPF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
PF07496. zf-CW. 1 hit.
[Graphical view]
SUPFAMiSSF46689. SSF46689. 1 hit.
SSF51905. SSF51905. 2 hits.
PROSITEiPS50934. SWIRM. 1 hit.
PS51050. ZF_CW. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM1B_HUMAN
AccessioniPrimary (citable) accession number: Q8NB78
Secondary accession number(s): A2A2C5
, A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q96EL7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 25, 2006
Last sequence update: January 11, 2011
Last modified: November 30, 2016
This is version 125 of the entry and version 3 of the sequence. [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. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  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. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.