O60341 (KDM1A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Lysine-specific histone demethylase 1A
EC=1.-.-.-

Alternative name(s):
BRAF35-HDAC complex protein BHC110
Flavin-containing amine oxidase domain-containing protein 2

Gene names

Name:	KDM1A
Synonyms:	AOF2, KDM1, KIAA0601, LSD1

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	852 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Histone demethylase that demethylates both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) H3K4me. May play a role in the repression of neuronal genes. Alone, it is unable to demethylate H3K4me on nucleosomes and requires the presence of RCOR1/CoREST to achieve such activity. Also acts as a coactivator of androgen receptor (ANDR)-dependent transcription, by being recruited to ANDR target genes and mediating demethylation of H3K9me, a specific tag for epigenetic transcriptional repression. The presence of PRKCB in ANDR-containing complexes, which mediates phosphorylation of 'Thr-6' of histone H3 (H3T6ph), a specific tag that prevents demethylation H3K4me, prevents H3K4me demethylase activity of KDM1A. Demethylates di-methylated 'Lys-370' of p53/TP53 which prevents interaction of p53/TP53 with TP53BP1 and represses p53/TP53-mediated transcriptional activation. Demethylates and stabilizes the DNA methylase DNMT1. Required for gastrulation during embryogenesis. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Effector of SNAI1-mediated transcription repression of E-cadherin/CDH1, CDN7 and KRT8. Required for the maintenance of the silenced state of the SNAI1 target genes E-cadherin/CDH1 and CDN7. Ref.5 Ref.8 Ref.12 Ref.15 Ref.22 Ref.23
Cofactor	FAD. Ref.8 Ref.9
Subunit structure	Component of a RCOR/GFI/KDM1A/HDAC complex. Interacts directly with GFI1 and GFI1B By similarity. Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, RCOR1/CoREST strongly enhances the demethylase activity and protects it from the proteasome while PHF21A/BHC80 inhibits the demethylase activity. Interacts with the androgen receptor (AR). Interacts with ASXL1. Interacts with SNAI1 (via SNAG domain). Ref.5 Ref.6 Ref.7 Ref.10 Ref.11 Ref.12 Ref.21 Ref.23
Subcellular location	Nucleus Ref.6 Ref.12.
Tissue specificity	Ubiquitously expressed. Ref.12
Domain	The SWIRM domain may act as an anchor site for a histone tail. Ref.29
Sequence similarities	Belongs to the flavin monoamine oxidase family. Contains 1 SWIRM domain.
Biophysicochemical properties	Kinetic parameters: KM=3.0 µM for H3 monomethyl-K4 Ref.13 KM=4.2 µM for H3 dimethyl-K4 KM=3.9 µM for H3 monomethyl-K4-monomethyl-K9 KM=17.5 µM for monomethyl-K4-acetyl-K9
Sequence caution	The sequence BAA25527.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Coiled coil
Ligand	FAD
Molecular function	Chromatin regulator Developmental protein Oxidoreductase Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	blood coagulation Traceable author statement. Source: Reactome cell proliferation Inferred from electronic annotation. Source: Compara granulocyte differentiation Inferred from electronic annotation. Source: Compara in utero embryonic development Inferred from electronic annotation. Source: Compara muscle cell development Inferred from sequence or structural similarity PubMed 20833138. Source: BHF-UCL negative regulation of DNA binding Inferred by curator Ref.15. Source: BHF-UCL negative regulation of DNA damage response, signal transduction by p53 class mediator Inferred from mutant phenotype Ref.15. Source: BHF-UCL negative regulation of apoptotic process Inferred from mutant phenotype Ref.15. Source: BHF-UCL negative regulation of histone H3-K4 methylation Inferred from electronic annotation. Source: Compara negative regulation of histone H3-K9 methylation Inferred from electronic annotation. Source: Compara negative regulation of protein binding Inferred from mutant phenotype Ref.15. Source: BHF-UCL negative regulation of sequence-specific DNA binding transcription factor activity Inferred from direct assay PubMed 19497860. Source: BHF-UCL negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype Ref.15. Source: BHF-UCL pituitary gland development Inferred from electronic annotation. Source: Compara positive regulation of erythrocyte differentiation Inferred from electronic annotation. Source: Compara positive regulation of hormone biosynthetic process Inferred from electronic annotation. Source: Compara positive regulation of megakaryocyte differentiation Inferred from electronic annotation. Source: Compara positive regulation of neural precursor cell proliferation Inferred from electronic annotation. Source: Compara positive regulation of sequence-specific DNA binding transcription factor activity Inferred from direct assay PubMed 20833138. Source: BHF-UCL positive regulation of stem cell proliferation Inferred from electronic annotation. Source: Compara positive regulation of transcription from RNA polymerase II promoter Inferred from direct assay PubMed 20833138. Source: BHF-UCL regulation of primitive erythrocyte differentiation Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nuclear chromatin Inferred from direct assay PubMed 17277772. Source: BHF-UCL transcription factor complex Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	MRF binding Inferred from direct assay PubMed 20833138. Source: BHF-UCL androgen receptor binding Inferred from direct assay Ref.12. Source: UniProtKB chromatin binding Inferred from direct assay Ref.12Ref.22. Source: UniProtKB flavin adenine dinucleotide binding Inferred from direct assay Ref.8. Source: UniProtKB histone demethylase activity (H3-K9 specific) Inferred from direct assay Ref.12Ref.22. Source: UniProtKB histone demethylase activity (H3-dimethyl-K4 specific) Inferred from direct assay Ref.22. Source: UniProtKB ligand-dependent nuclear receptor transcription coactivator activity Inferred from mutant phenotype Ref.12. Source: UniProtKB oxidoreductase activity Inferred from direct assay Ref.8. Source: UniProtKB sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: Compara transcription regulatory region DNA binding Inferred from sequence or structural similarity. Source: BHF-UCL
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ASXL1	Q8IXJ9	2	EBI-710124,EBI-1646500
Asxl1	P59598	2	EBI-710124,EBI-5743705	From a different organism.
CHD3	Q12873	4	EBI-710124,EBI-523590
HIST3H3	Q16695	2	EBI-710124,EBI-358900
IMMT	Q16891	2	EBI-710124,EBI-473801
RCOR1	Q9UKL0	2	EBI-710124,EBI-926563
SNAI1	O95863	4	EBI-710124,EBI-1045459

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O60341-1)

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: O60341-2)

The sequence of this isoform differs from the canonical sequence as follows:
     173-173: G → GQAGGLQDDSSGGYGDGQASG
     369-369: A → ADTVK

Note: No experimental confirmation available.

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 852

852

Lysine-specific histone demethylase 1A

PRO_0000099881

Regions

Domain

174 – 273

100

SWIRM

Nucleotide binding

281 – 309

29

FAD Potential

Nucleotide binding

332 – 333

2

FAD

Nucleotide binding

810 – 811

2

FAD

Region

300 – 852

553

Demethylase activity

Coiled coil

110 – 151

42

Potential

Coiled coil

428 – 514

87

Potential

Compositional bias

7 – 42

36

Ala-rich

Compositional bias

152 – 156

5

Poly-Pro

Sites

Binding site

289

1

FAD

Binding site

308

1

FAD

Binding site

310

1

FAD

Binding site

316

1

FAD

Binding site

801

1

FAD

Amino acid modifications

Modified residue

104

1

Phosphothreonine Ref.18 Ref.20

Modified residue

126

1

Phosphoserine Ref.18

Modified residue

131

1

Phosphoserine Ref.14 Ref.17 Ref.18 Ref.19 Ref.20 Ref.24 Ref.26

Modified residue

137

1

Phosphoserine Ref.20 Ref.24 Ref.26

Modified residue

166

1

Phosphoserine Ref.16 Ref.18 Ref.24 Ref.26

Modified residue

849

1

Phosphoserine Ref.18 Ref.24

Natural variations

Alternative sequence

173

1

G → GQAGGLQDDSSGGYGDGQAS G in isoform 2.

VSP_011198

Alternative sequence

369

1

A → ADTVK in isoform 2.

VSP_011199

Experimental info

Mutagenesis

535

1

N → A: Strongly reduces demethylase activity. Ref.28

Mutagenesis

564

1

H → A: Strongly reduces demethylase activity. Ref.28

Mutagenesis

661

1

K → A: Abolishes histone demethylase activity. Ref.11

Mutagenesis

761

1

Y → A: Strongly reduces demethylase activity. Ref.28

Sequence conflict

78

1

P → Q in AAH40194. Ref.3

Sequence conflict

405

1

P → H in AAH48134. Ref.3

Sequence conflict

669

1

V → A in CAD38675. Ref.4

Sequence conflict

814

1

A → V in AAH16639. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

852

Helix Strand Turn

Details...

Helix

173 – 180

8

Beta strand

181 – 183

3

Beta strand

185 – 187

3

Helix

190 – 195

6

Helix

197 – 200

4

Helix

204 – 222

19

Helix

231 – 237

7

Helix

242 – 244

3

Helix

246 – 258

13

Beta strand

261 – 263

3

Beta strand

265 – 267

3

Beta strand

280 – 284

5

Helix

288 – 299

12

Beta strand

303 – 307

5

Beta strand

309 – 314

6

Beta strand

319 – 322

4

Beta strand

325 – 330

6

Beta strand

333 – 335

3

Helix

341 – 349

9

Beta strand

353 – 355

3

Beta strand

367 – 369

3

Helix

372 – 393

22

Turn

394 – 396

3

Beta strand

400 – 405

6

Helix

408 – 456

49

Turn

457 – 461

5

Helix

476 – 487

12

Turn

488 – 490

3

Helix

491 – 497

7

Helix

499 – 511

13

Beta strand

518 – 521

4

Helix

523 – 539

17

Helix

544 – 546

3

Turn

549 – 555

7

Helix

556 – 558

3

Beta strand

565 – 567

3

Helix

573 – 578

6

Turn

579 – 581

3

Beta strand

583 – 585

3

Beta strand

588 – 596

9

Beta strand

599 – 608

10

Beta strand

613 – 623

11

Helix

627 – 631

5

Beta strand

636 – 641

6

Helix

645 – 653

9

Beta strand

654 – 656

3

Beta strand

660 – 665

6

Beta strand

676 – 680

5

Beta strand

683 – 685

3

Turn

686 – 689

4

Beta strand

690 – 695

6

Beta strand

698 – 707

10

Helix

710 – 715

6

Helix

720 – 735

16

Turn

737 – 739

3

Beta strand

744 – 748

5

Turn

751 – 753

3

Turn

755 – 757

3

Beta strand

758 – 760

3

Helix

771 – 777

7

Beta strand

796 – 798

3

Helix

801 – 803

3

Beta strand

805 – 807

3

Helix

811 – 829

19

Helix

833 – 835

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified August 16, 2004. Version 2. Checksum: A61CEDE51E4E0C1D	FASTA	852	92,903
	10 20 30 40 50 60 MLSGKKAAAA AAAAAAAATG TEAGPGTAGG SENGSEVAAQ PAGLSGPAEV GPGAVGERTP 70 80 90 100 110 120 RKKEPPRASP PGGLAEPPGS AGPQAGPTVV PGSATPMETG IAETPEGRRT SRRKRAKVEY 130 140 150 160 170 180 REMDESLANL SEDEYYSEEE RNAKAEKEKK LPPPPPQAPP EEENESEPEE PSGVEGAAFQ 190 200 210 220 230 240 SRLPHDRMTS QEAACFPDII SGPQQTQKVF LFIRNRTLQL WLDNPKIQLT FEATLQQLEA 250 260 270 280 290 300 PYNSDTVLVH RVHSYLERHG LINFGIYKRI KPLPTKKTGK VIIIGSGVSG LAAARQLQSF 310 320 330 340 350 360 GMDVTLLEAR DRVGGRVATF RKGNYVADLG AMVVTGLGGN PMAVVSKQVN MELAKIKQKC 370 380 390 400 410 420 PLYEANGQAV PKEKDEMVEQ EFNRLLEATS YLSHQLDFNV LNNKPVSLGQ ALEVVIQLQE 430 440 450 460 470 480 KHVKDEQIEH WKKIVKTQEE LKELLNKMVN LKEKIKELHQ QYKEASEVKP PRDITAEFLV 490 500 510 520 530 540 KSKHRDLTAL CKEYDELAET QGKLEEKLQE LEANPPSDVY LSSRDRQILD WHFANLEFAN 550 560 570 580 590 600 ATPLSTLSLK HWDQDDDFEF TGSHLTVRNG YSCVPVALAE GLDIKLNTAV RQVRYTASGC 610 620 630 640 650 660 EVIAVNTRST SQTFIYKCDA VLCTLPLGVL KQQPPAVQFV PPLPEWKTSA VQRMGFGNLN 670 680 690 700 710 720 KVVLCFDRVF WDPSVNLFGH VGSTTASRGE LFLFWNLYKA PILLALVAGE AAGIMENISD 730 740 750 760 770 780 DVIVGRCLAI LKGIFGSSAV PQPKETVVSR WRADPWARGS YSYVAAGSSG NDYDLMAQPI 790 800 810 820 830 840 TPGPSIPGAP QPIPRLFFAG EHTIRNYPAT VHGALLSGLR EAGRIADQFL GAMYTLPRQA 850 TPGVPAQQSP SM
	Isoform 2 [UniParc]. Checksum: 966CA72A70F68111	FASTA	876	95,155
	10 20 30 40 50 60 MLSGKKAAAA AAAAAAAATG TEAGPGTAGG SENGSEVAAQ PAGLSGPAEV GPGAVGERTP 70 80 90 100 110 120 RKKEPPRASP PGGLAEPPGS AGPQAGPTVV PGSATPMETG IAETPEGRRT SRRKRAKVEY 130 140 150 160 170 180 REMDESLANL SEDEYYSEEE RNAKAEKEKK LPPPPPQAPP EEENESEPEE PSGQAGGLQD 190 200 210 220 230 240 DSSGGYGDGQ ASGVEGAAFQ SRLPHDRMTS QEAACFPDII SGPQQTQKVF LFIRNRTLQL 250 260 270 280 290 300 WLDNPKIQLT FEATLQQLEA PYNSDTVLVH RVHSYLERHG LINFGIYKRI KPLPTKKTGK 310 320 330 340 350 360 VIIIGSGVSG LAAARQLQSF GMDVTLLEAR DRVGGRVATF RKGNYVADLG AMVVTGLGGN 370 380 390 400 410 420 PMAVVSKQVN MELAKIKQKC PLYEANGQAD TVKVPKEKDE MVEQEFNRLL EATSYLSHQL 430 440 450 460 470 480 DFNVLNNKPV SLGQALEVVI QLQEKHVKDE QIEHWKKIVK TQEELKELLN KMVNLKEKIK 490 500 510 520 530 540 ELHQQYKEAS EVKPPRDITA EFLVKSKHRD LTALCKEYDE LAETQGKLEE KLQELEANPP 550 560 570 580 590 600 SDVYLSSRDR QILDWHFANL EFANATPLST LSLKHWDQDD DFEFTGSHLT VRNGYSCVPV 610 620 630 640 650 660 ALAEGLDIKL NTAVRQVRYT ASGCEVIAVN TRSTSQTFIY KCDAVLCTLP LGVLKQQPPA 670 680 690 700 710 720 VQFVPPLPEW KTSAVQRMGF GNLNKVVLCF DRVFWDPSVN LFGHVGSTTA SRGELFLFWN 730 740 750 760 770 780 LYKAPILLAL VAGEAAGIME NISDDVIVGR CLAILKGIFG SSAVPQPKET VVSRWRADPW 790 800 810 820 830 840 ARGSYSYVAA GSSGNDYDLM AQPITPGPSI PGAPQPIPRL FFAGEHTIRN YPATVHGALL 850 860 870 SGLREAGRIA DQFLGAMYTL PRQATPGVPA QQSPSM

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro." Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 5:31-39(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain.
[2]	"The DNA sequence and biological annotation of human chromosome 1." Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R. Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2). Tissue: Brain, Skin and Testis.
[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 245-852 (ISOFORM 1). Tissue: Brain.
[5]	"A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes." Hakimi M.-A., Bochar D.A., Chenoweth J., Lane W.S., Mandel G., Shiekhattar R. Proc. Natl. Acad. Sci. U.S.A. 99:7420-7425(2002) [PubMed] [Europe PMC] [Abstract] Cited for: PARTIAL PROTEIN SEQUENCE, INTERACTION WITH A HISTONE DEACETYLASE-CONTAINING COMPLEX, FUNCTION.
[6]	"Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1." Humphrey G.W., Wang Y., Russanova V.R., Hirai T., Qin J., Nakatani Y., Howard B.H. J. Biol. Chem. 276:6817-6824(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH THE HDAC1 COMPLEX, MASS SPECTROMETRY, SUBCELLULAR LOCATION.
[7]	"A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes." Hakimi M.-A., Dong Y., Lane W.S., Speicher D.W., Shiekhattar R. J. Biol. Chem. 278:7234-7239(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH A HISTONE DEACETYLASE-CONTAINING COMPLEX, MASS SPECTROMETRY.
[8]	"Histone demethylation mediated by the nuclear amine oxidase homolog LSD1." Shi Y.-J., Lan F., Matson C., Mulligan P., Whetstine J.R., Cole P.A., Casero R.A., Shi Y. Cell 119:941-953(2004) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME ACTIVITY, FUNCTION, COFACTOR.
[9]	"Histone demethylation catalysed by LSD1 is a flavin-dependent oxidative process." Forneris F., Binda C., Vanoni M.A., Mattevi A., Battaglioli E. FEBS Lett. 579:2203-2207(2005) [PubMed] [Europe PMC] [Abstract] Cited for: ENZYME ACTIVITY, COFACTOR.
[10]	"Regulation of LSD1 histone demethylase activity by its associated factors." Shi Y.-J., Matson C., Lan F., Iwase S., Baba T., Shi Y. Mol. Cell 19:857-864(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RCOR1 AND PHF21A.
[11]	"An essential role for CoREST in nucleosomal histone 3 lysine 4 demethylation." Lee M.G., Wynder C., Cooch N., Shiekhattar R. Nature 437:432-435(2005) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RCOR1, MUTAGENESIS OF LYS-661.
[12]	"LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription." Metzger E., Wissmann M., Yin N., Mueller J.M., Schneider R., Peters A.H.F.M., Guenther T., Buettner R., Schuele R. Nature 437:436-439(2005) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH ANDR.
[13]	"Human histone demethylase LSD1 reads the histone code." Forneris F., Binda C., Vanoni M.A., Battaglioli E., Mattevi A. J. Biol. Chem. 280:41360-41365(2005) [PubMed] [Europe PMC] [Abstract] Cited for: BIOPHYSICOCHEMICAL PROPERTIES.
[14]	"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks." Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M. Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[15]	"p53 is regulated by the lysine demethylase LSD1." Huang J., Sengupta R., Espejo A.B., Lee M.G., Dorsey J.A., Richter M., Opravil S., Shiekhattar R., Bedford M.T., Jenuwein T., Berger S.L. Nature 449:105-108(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[16]	"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-166, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[17]	"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle." Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M. Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[18]	"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 THR-104; SER-126; SER-131; SER-166 AND SER-849, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[19]	"Large-scale proteomics analysis of the human kinome." Oppermann F.S., Gnad F., Olsen J.V., Hornberger R., Greff Z., Keri G., Mann M., Daub H. Mol. Cell. Proteomics 8:1751-1764(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131, MASS SPECTROMETRY.
[20]	"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions." Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K. Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-104; SER-131 AND SER-137, MASS SPECTROMETRY. Tissue: Leukemic T-cell.
[21]	"ASXL1 represses retinoic acid receptor-mediated transcription through associating with HP1 and LSD1." Lee S.W., Cho Y.S., Na J.M., Park U.H., Kang M., Kim E.J., Um S.J. J. Biol. Chem. 285:18-29(2010) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH ASXL1.
[22]	"Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4." Metzger E., Imhof A., Patel D., Kahl P., Hoffmeyer K., Friedrichs N., Muller J.M., Greschik H., Kirfel J., Ji S., Kunowska N., Beisenherz-Huss C., Gunther T., Buettner R., Schule R. Nature 464:792-796(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION.
[23]	"Requirement of the histone demethylase LSD1 in Snai1-mediated transcriptional repression during epithelial-mesenchymal transition." Lin T., Ponn A., Hu X., Law B.K., Lu J. Oncogene 29:4896-4904(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, INTERACTION WITH SNAI.
[24]	"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-131; SER-137; SER-166 AND SER-849, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[25]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[26]	"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation." Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B. Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-131; SER-137 AND SER-166, MASS SPECTROMETRY.
[27]	"Structural basis for CoREST-dependent demethylation of nucleosomes by the human LSD1 histone demethylase." Yang M., Gocke C.B., Luo X., Borek D., Tomchick D.R., Machius M., Otwinowski Z., Yu H. Mol. Cell 23:377-387(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.57 ANGSTROMS) OF 171-836 IN COMPLEX WITH FAD AND RCOR1.
[28]	"Crystal structure of human histone lysine-specific demethylase 1 (LSD1)." Chen Y., Yang Y., Wang F., Wan K., Yamane K., Zhang Y., Lei M. Proc. Natl. Acad. Sci. U.S.A. 103:13956-13961(2006) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 172-835 IN COMPLEX WITH FAD, MUTAGENESIS OF ASN-535; HIS-564 AND TYR-761.
[29]	"Solution structure of the SWIRM domain of human histone demethylase LSD1." Tochio N., Umehara T., Koshiba S., Inoue M., Yabuki T., Aoki M., Seki E., Watanabe S., Tomo Y., Hanada M., Ikari M., Sato M., Terada T., Nagase T., Ohara O., Shirouzu M., Tanaka A., Kigawa T., Yokoyama S. Structure 14:457-468(2006) [PubMed] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 166-285, DOMAIN.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB011173 mRNA. Translation: BAA25527.1. Different initiation.
AL031428 Genomic DNA. Translation: CAI19707.2.
AL031428 Genomic DNA. Translation: CAI19708.2.
BC016639 mRNA. Translation: AAH16639.1.
BC025362 mRNA. Translation: AAH25362.1.
BC040194 mRNA. Translation: AAH40194.3.
BC048134 mRNA. Translation: AAH48134.2.
AL833812 mRNA. Translation: CAD38675.2.

IPI

IPI00217540.
IPI00456631.

RefSeq

NP_001009999.1. NM_001009999.2.
NP_055828.2. NM_015013.3.

UniGene

Hs.591518.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2COM	NMR	-	A	169-279	[»]
2DW4	X-ray	2.30	A	172-831	[»]
2EJR	X-ray	2.70	A	172-833	[»]
2H94	X-ray	2.90	A	172-835	[»]
2HKO	X-ray	2.80	A	172-835	[»]
2IW5	X-ray	2.57	A	171-836	[»]
2L3D	NMR	-	A	174-273	[»]
2UXN	X-ray	2.72	A	171-836	[»]
2UXX	X-ray	2.74	A	171-836	[»]
2V1D	X-ray	3.10	A	123-852	[»]
2X0L	X-ray	3.00	A	123-852	[»]
2XAF	X-ray	3.25	A	1-852	[»]
2XAG	X-ray	3.10	A	1-852	[»]
2XAH	X-ray	3.10	A	1-852	[»]
2XAJ	X-ray	3.30	A	1-852	[»]
2XAQ	X-ray	3.20	A	1-852	[»]
2XAS	X-ray	3.20	A	1-852	[»]
2Y48	X-ray	3.00	A	123-852	[»]
2Z3Y	X-ray	2.25	A	172-833	[»]
2Z5U	X-ray	2.25	A	172-833	[»]
3ABT	X-ray	3.20	A	172-833	[»]
3ABU	X-ray	3.10	A	172-833	[»]

ProteinModelPortal

O60341.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-34641N.

IntAct

O60341. 32 interactions.

MINT

MINT-1372817.

PTM databases

PhosphoSite

O60341.

Proteomic databases

PaxDb

O60341.

PRIDE

O60341.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000356634; ENSP00000349049; ENSG00000004487.
ENST00000400181; ENSP00000383042; ENSG00000004487.

GeneID

23028.

KEGG

hsa:23028.

UCSC

uc001bgi.2. human.
uc001bgj.2. human.

Organism-specific databases

CTD

23028.

GeneCards

GC01P023347.

HGNC

HGNC:29079. KDM1A.

HPA

CAB005884.

MIM

609132. gene.

neXtProt

NX_O60341.

PharmGKB

PA165751392.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG1231.

KO

K11450.

OMA

HRIHSYL.

OrthoDB

EOG4R7V9M.

Enzyme and pathway databases

Pathway_Interaction_DB

ar_pathway. Coregulation of Androgen receptor activity.

Reactome

REACT_604. Hemostasis.

Gene expression databases

ArrayExpress

O60341.

Bgee

O60341.

CleanEx

HS_AOF2.

Genevestigator

O60341.

GermOnline

ENSG00000004487. Homo sapiens.

Family and domain databases

Gene3D

1.10.10.10. 1 hit.

InterPro

IPR002937. Amino_oxidase.
IPR017366. Hist_Lys-spec_deMease.
IPR009057. Homeodomain-like.
IPR007526. SWIRM.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]

Pfam

PF01593. Amino_oxidase. 1 hit.
PF04433. SWIRM. 1 hit.
[Graphical view]

PIRSF

PIRSF038051. Histone_Lys-demethylase. 1 hit.

SUPFAM

SSF46689. Homeodomain_like. 1 hit.

PROSITE

PS50934. SWIRM. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

BindingDB

O60341.

ChEMBL

CHEMBL6136.

ChiTaRS

KDM1A. human.

EvolutionaryTrace

O60341.

GenomeRNAi

23028.

NextBio

43998.

SOURCE

Search...

Entry information

Entry name

KDM1A_HUMAN

Accession

Primary (citable) accession number: O60341
Secondary accession number(s): A8MWP9 , Q5TH94, Q5TH95, Q86VT7, Q8IXK4, Q8NDP6, Q8TAZ3, Q96AW4

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 16, 2004
Last sequence update:	August 16, 2004
Last modified:	May 1, 2013
This is version 134 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.