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Q8NB78 (KDM1B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 99. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:KDM1B
Synonyms:AOF1, C6orf193, LSD2
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length822 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

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 By similarity.

Cofactor

FAD By similarity.

Subunit structure

Does not form a complex with RCOR1/CoREST By similarity.

Subcellular location

Nucleus By similarity.

Domain

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

Sequence similarities

Belongs to the flavin monoamine oxidase family.

Contains 1 CW-type zinc finger.

Contains 1 SWIRM domain.

Sequence caution

The sequence BAC03663.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainZinc-finger
   LigandFAD
Flavoprotein
Metal-binding
Zinc
   Molecular functionChromatin regulator
Developmental protein
Oxidoreductase
Repressor
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA methylation involved in gamete generation

Inferred from electronic annotation. Source: Ensembl

histone H3-K4 demethylation

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

multicellular organismal development

Inferred from electronic annotation. Source: UniProtKB-KW

regulation of DNA methylation

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

regulation of gene expression by genetic imprinting

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

flavin adenine dinucleotide binding

Inferred from electronic annotation. Source: Ensembl

histone demethylase activity (H3-dimethyl-K4 specific)

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

histone demethylase activity (H3-monomethyl-K4 specific)

Inferred from sequence or structural similarity PubMed 19727073. Source: UniProtKB

oxidoreductase activity

Inferred from electronic annotation. Source: UniProtKB-KW

zinc ion binding

Inferred from electronic annotation. Source: Ensembl

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8NB78-1)

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.
Isoform 2 (identifier: Q8NB78-2)

The sequence of this isoform differs from the canonical sequence as follows:
     192-323: Missing.
     453-552: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q8NB78-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-647: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 822822Lysine-specific histone demethylase 1B
PRO_0000247336

Regions

Domain275 – 37399SWIRM
Zinc finger133 – 19361CW-type
Nucleotide binding383 – 43957FAD Potential

Amino acid modifications

Modified residue171Phosphoserine Ref.5 Ref.6 Ref.7
Modified residue2471Phosphoserine Ref.7

Natural variations

Alternative sequence1 – 647647Missing in isoform 4.
VSP_019963
Alternative sequence192 – 323132Missing in isoform 2.
VSP_019964
Alternative sequence453 – 552100Missing in isoform 2.
VSP_019965

Experimental info

Sequence conflict6511I → T in BAC86124. Ref.1
Sequence conflict794 – 7952Missing in CAH10499. Ref.4

Secondary structure

......................................................................................................................................................... 822
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 11, 2011. Version 3.
Checksum: 6C0A9BD6B2CEA2EA

FASTA82292,098
        10         20         30         40         50         60 
MATPRGRTKK KASFDHSPDS LPLRSSGRQA KKKATETTDE DEDGGSEKKY RKCEKAGCTA 

        70         80         90        100        110        120 
TCPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY RSHKDGYDKY TTWKKIWTSN 

       130        140        150        160        170        180 
GKTEPSPKAF MADQQLPYWV QCTKPECRKW RQLTKEIQLT PQIAKTYRCG MKPNTAIKPE 

       190        200        210        220        230        240 
TSDHCSLPED LRVLEVSNHW WYSMLILPPL LKDSVAAPLL SAYYPDCVGM SPSCTSTNRA 

       250        260        270        280        290        300 
AATGNASPGK LEHSKAALSV HVPGMNRYFQ PFYQPNECGK ALCVRPDVME LDELYEFPEY 

       310        320        330        340        350        360 
SRDPTMYLAL RNLILALWYT NCKEALTPQK CIPHIIVRGL VRIRCVQEVE RILYFMTRKG 

       370        380        390        400        410        420 
LINTGVLSVG ADQYLLPKDY HNKSVIIIGA GPAGLAAARQ LHNFGIKVTV LEAKDRIGGR 

       430        440        450        460        470        480 
VWDDKSFKGV TVGRGAQIVN GCINNPVALM CEQLGISMHK FGERCDLIQE GGRITDPTID 

       490        500        510        520        530        540 
KRMDFHFNAL LDVVSEWRKD KTQLQDVPLG EKIEEIYKAF IKESGIQFSE LEGQVLQFHL 

       550        560        570        580        590        600 
SNLEYACGSN LHQVSARSWD HNEFFAQFAG DHTLLTPGYS VIIEKLAEGL DIQLKSPVQC 

       610        620        630        640        650        660 
IDYSGDEVQV TTTDGTGYSA QKVLVTVPLA LLQKGAIQFN PPLSEKKMKA INSLGAGIIE 

       670        680        690        700        710        720 
KIALQFPYRF WDSKVQGADF FGHVPPSASK RGLFAVFYDM DPQKKHSVLM SVIAGEAVAS 

       730        740        750        760        770        780 
VRTLDDKQVL QQCMATLREL FKEQEVPDPT KYFVTRWSTD PWIQMAYSFV KTGGSGEAYD 

       790        800        810        820 
IIAEDIQGTV FFAGEATNRH FPQTVTGAYL SGVREASKIA AF 

« Hide

Isoform 2 [UniParc].

Checksum: AFDC638DFD727A9E
Show »

FASTA59065,717
Isoform 4 [UniParc].

Checksum: 5571123B00CDE9E8
Show »

FASTA17519,428

References

[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 2 AND 4), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 185-822 (ISOFORM 1).
Tissue: Brain and Tongue.
[2]"The DNA sequence and analysis of human chromosome 6."
Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D. expand/collapse author list , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 624-822 (ISOFORM 1).
Tissue: Cervix.
[5]"Combining protein-based IMAC, peptide-based IMAC, and MudPIT for efficient phosphoproteomic analysis."
Cantin G.T., Yi W., Lu B., Park S.K., Xu T., Lee J.-D., Yates J.R. III
J. Proteome Res. 7:1346-1351(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[6]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17 AND SER-247, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_694587.3. NM_153042.3.
XP_005248983.1. XM_005248926.1.
UniGeneHs.709336.

3D structure databases

PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortalQ8NB78.
SMRQ8NB78. Positions 49-822.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid128743. 9 interactions.
IntActQ8NB78. 1 interaction.
STRING9606.ENSP00000297792.

Chemistry

BindingDBQ8NB78.
ChEMBLCHEMBL1938208.

PTM databases

PhosphoSiteQ8NB78.

Polymorphism databases

DMDM317373434.

Proteomic databases

PaxDbQ8NB78.
PRIDEQ8NB78.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000297792; ENSP00000297792; ENSG00000165097. [Q8NB78-2]
GeneID221656.
KEGGhsa:221656.
UCSCuc003ncn.1. human. [Q8NB78-2]
uc003nco.1. human. [Q8NB78-1]
uc003ncp.1. human. [Q8NB78-4]

Organism-specific databases

CTD221656.
GeneCardsGC06P018156.
H-InvDBHIX0005608.
HGNCHGNC:21577. KDM1B.
HPAHPA031269.
HPA055597.
MIM613081. gene.
neXtProtNX_Q8NB78.
PharmGKBPA162379723.
PA165617946.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG1231.
HOGENOMHOG000230870.
HOVERGENHBG079963.
InParanoidQ8NB78.
OrthoDBEOG7X9G66.
PhylomeDBQ8NB78.
TreeFamTF352593.

Gene expression databases

ArrayExpressQ8NB78.
BgeeQ8NB78.
CleanExHS_AOF1.
GenevestigatorQ8NB78.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR002937. Amino_oxidase.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
IPR011124. Znf_CW.
[Graphical view]
PfamPF01593. Amino_oxidase. 1 hit.
PF07496. zf-CW. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS50934. SWIRM. 1 hit.
PS51050. ZF_CW. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GenomeRNAi221656.
NextBio91405.
PROQ8NB78.
SOURCESearch...

Entry information

Entry nameKDM1B_HUMAN
AccessionPrimary (citable) accession number: Q8NB78
Secondary accession number(s): A2A2C5 expand/collapse secondary AC list , A2A2C6, Q5TGV3, Q6AI15, Q6ZUU4, Q8N258, Q96EL7
Entry history
Integrated into UniProtKB/Swiss-Prot: July 25, 2006
Last sequence update: January 11, 2011
Last modified: April 16, 2014
This is version 99 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 6

Human chromosome 6: entries, gene names and cross-references to MIM