Reviewed, UniProtKB/Swiss-Prot O75164 (KDM4A_HUMAN)

Names and origin

Protein names

Recommended name:
    Lysine-specific demethylase 4A
    EC=1.14.11.-
Alternative name(s):
    JmjC domain-containing histone demethylation protein 3A
    Jumonji domain-containing protein 2A

Gene names

Name:	KDM4A
Synonyms:	JHDM3A, JMJD2, JMJD2A, KIAA0677

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	1064 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Participates in transcriptional repression of ASCL2 and E2F-responsive promoters via the recruitment of histone deacetylases and NCOR1, respectively. Ref.5 Ref.7
Cofactor	Binds 1 Fe2+ ion per subunit. Ref.7
Subunit structure	Interacts with histone deacetylase proteins HDAC1, HDAC2 and HDAC3. Interacts with RB and NCOR1. Interacts with HTLV-1 Tax protein. Ref.5 Ref.4
Subcellular location	Nucleus.
Tissue specificity	Ubiquitous. Ref.4
Domain	The 2 Tudor domains recognize and bind methylated histone H3 'Lys-4' residue. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails. Trimethylated H3 'Lys-4' is bound in a cage of 3 aromatic residues, 2 of which are from the Tudor domain 2, while the binding specificity is determined by side-chain interactions involving residues from the Tudor domain 1. The Tudor domains are able to bind trimethylated histone H3 'Lys-4', trimethylated histone H3 'Lys-9', di- and trimethylated H4 'Lys-20'. Ref.7 Ref.8 Ref.10
Sequence similarities	Belongs to the JHDM3 histone demethylase family. Contains 1 JmjC domain. Contains 1 JmjN domain. Contains 2 PHD-type zinc fingers. Contains 2 Tudor domains.

Ontologies

Keywords
Biological process	Host-virus interaction Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Polymorphism
Domain	Repeat Zinc-finger
Ligand	Iron Metal-binding Zinc
Molecular function	Chromatin regulator Dioxygenase Oxidoreductase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	histone demethylation Ref.5 Inferred from direct assay. Source: UniProtKB interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW oxidation reduction Inferred from electronic annotation. Source: UniProtKB-KW regulation of transcription Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from direct assay. Source: HPA nucleolus Inferred from direct assay. Source: HPA
Molecular function	histone demethylase activity (H3-K36 specific) Ref.5 Inferred from direct assay. Source: UniProtKB iron ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid binding Inferred from electronic annotation. Source: InterPro oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct transcription repressor activity Ref.5 Inferred from direct assay. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
HIST3H3	Q16695	3	EBI-936709,EBI-358900

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 1064

1064

Lysine-specific demethylase 4A

PRO_0000183172

Regions

Domain

14 – 56

43

JmjN

Domain

142 – 308

167

JmjC

Domain

897 – 954

58

Tudor 1

Domain

955 – 1011

57

Tudor 2

Zinc finger

709 – 767

59

PHD-type 1

Zinc finger

829 – 885

57

PHD-type 2

Region

597 – 638

42

Interaction with NCOR1

Sites

Metal binding

188

1

Iron; catalytic

Metal binding

190

1

Iron; catalytic

Metal binding

234

1

Zinc

Metal binding

240

1

Zinc

Metal binding

276

1

Iron; catalytic

Metal binding

306

1

Zinc

Metal binding

308

1

Zinc

Binding site

132

1

Alpha-ketoglutarate

Binding site

198

1

Alpha-ketoglutarate

Binding site

206

1

Alpha-ketoglutarate

Binding site

945

1

Histone H3-K4Me3

Binding site

967

1

Histone H3-K4Me3

Binding site

973

1

Histone H3-K4Me3

Amino acid modifications

Modified residue

547

1

Phosphotyrosine Ref.6

Natural variations

Natural variant

482

1

E → A: dbSNP rs586339.

VAR_023775

Natural variant

877

1

V → G: dbSNP rs12759032.

VAR_031217

Experimental info

Mutagenesis

133

1

G → A: Abolishes histone demethylase activity; when associated with A-138. Ref.9

Mutagenesis

138

1

G → A: Abolishes histone demethylase activity; when associated with A-138. Ref.9

Mutagenesis

165

1

G → A: Abolishes histone demethylase activity; when associated with A-165. Ref.9

Mutagenesis

170

1

G → A: Abolishes histone demethylase activity; when associated with A-165. Ref.9

Mutagenesis

188

1

H → A: Abolishes histone demethylase activity. Ref.7

Mutagenesis

288 – 289

2

ST → AI: Displays histone demethylase activity for both dimethylated and H3-K9Me3.

Mutagenesis

288 – 289

2

ST → TV, NV or GG: Abolishes histone demethylase activity.

Mutagenesis

945

1

D → A: Impairs binding to H3-K4Me3. Ref.10

Mutagenesis

945

1

D → R: Abolishes binding to H3-K4Me3. Ref.10

Mutagenesis

967

1

W → H: Abolishes binding to H3-K4Me3. Ref.10

Mutagenesis

973

1

Y → A: Abolishes binding to H3-K4Me3. Ref.10 Ref.9

Secondary structure

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1064

Helix Strand Turn

Details...

Helix

6 – 8

3

Turn

9 – 11

3

Beta strand

15 – 17

3

Helix

21 – 25

5

Helix

27 – 36

10

Helix

39 – 42

4

Beta strand

43 – 47

5

Beta strand

59 – 61

3

Beta strand

66 – 69

4

Beta strand

71 – 78

8

Beta strand

81 – 88

8

Helix

94 – 102

9

Turn

104 – 106

3

Helix

114 – 124

11

Beta strand

131 – 137

7

Helix

158 – 164

7

Turn

169 – 171

3

Beta strand

175 – 178

4

Beta strand

184 – 188

5

Helix

191 – 193

3

Beta strand

195 – 204

10

Beta strand

206 – 211

6

Helix

213 – 215

3

Helix

216 – 226

11

Helix

228 – 233

6

Helix

237 – 240

4

Beta strand

243 – 245

3

Helix

247 – 252

6

Beta strand

258 – 262

5

Beta strand

267 – 270

4

Beta strand

275 – 280

6

Beta strand

282 – 291

10

Helix

296 – 302

7

Helix

318 – 324

7

Helix

326 – 328

3

Helix

329 – 333

5

Helix

351 – 354

4

Beta strand

904 – 908

5

Beta strand

912 – 932

21

Beta strand

937 – 941

5

Helix

943 – 945

3

Helix

951 – 954

4

Beta strand

962 – 966

5

Beta strand

972 – 990

19

Beta strand

995 – 998

4

Helix

1000 – 1002

3

Sequences

	Sequence		Length	Mass (Da)
	O75164-1 [UniParc]. Last modified November 1, 1998. Version 1. Checksum: 54AA1EC0E579C78A	FASTA	1,064	120,720
	10 20 30 40 50 60 MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP KEWKPRASYD 70 80 90 100 110 120 DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI ANSDKYCTPR YSEFEELERK 130 140 150 160 170 180 YWKNLTFNPP IYGADVNGTL YEKHVDEWNI GRLRTILDLV EKESGITIEG VNTPYLYFGM 190 200 210 220 230 240 WKTSFAWHTE DMDLYSINYL HFGEPKSWYS VPPEHGKRLE RLAKGFFPGS AQSCEAFLRH 250 260 270 280 290 300 KMTLISPLML KKYGIPFDKV TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATRRWIEYG 310 320 330 340 350 360 KQAVLCSCRK DMVKISMDVF VRKFQPERYK LWKAGKDNTV IDHTLPTPEA AEFLKESELP 370 380 390 400 410 420 PRAGNEEECP EEDMEGVEDG EEGDLKTSLA KHRIGTKRHR VCLEIPQEVS QSELFPKEDL 430 440 450 460 470 480 SSEQYEMTEC PAALAPVRPT HSSVRQVEDG LTFPDYSDST EVKFEELKNV KLEEEDEEEE 490 500 510 520 530 540 QEAAALDLSV NPASVGGRLV FSGSKKKSSS SLGSGSSRDS ISSDSETSEP LSCRAQGQTG 550 560 570 580 590 600 VLTVHSYAKG DGRVTVGEPC TRKKGSAARS FSERELAEVA DEYMFSLEEN KKSKGRRQPL 610 620 630 640 650 660 SKLPRHHPLV LQECVSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN FEAEKEFNET 670 680 690 700 710 720 MAQQAPHCAV CMIFQTYHQV EFGGFNQNCG NASDLAPQKQ RTKPLIPEMC FTSTGCSTDI 730 740 750 760 770 780 NLSTPYLEED GTSILVSCKK CSVRVHASCY GVPPAKASED WMCSRCSANA LEEDCCLCSL 790 800 810 820 830 840 RGGALQRAND DRWVHVSCAV AILEARFVNI AERSPVDVSK IPLPRFKLKC IFCKKRRKRT 850 860 870 880 890 900 AGCCVQCSHG RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALQSIT 910 920 930 940 950 960 AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD CLQFGPPAEG 970 980 990 1000 1010 1020 EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR DDVYTLDEEL PKRVKSRLSV 1030 1040 1050 1060 ASDMRFNEIF TEKEVKQEKK RQRVINSRYR EDYIEPALYR AIME

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro." Ishikawa K., Nagase T., Suyama M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 5:169-176(1998) [PubMed: 9734811] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. 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: 16710414] [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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Placenta.
[4]	"Functional characterization of JMJD2A, a histone deacetylase- and retinoblastoma-binding protein." Gray S.G., Iglesias A.H., Lizcano F., Villanueva R., Camelo S., Jingu H., Teh B.T., Koibuchi N., Chin W.W., Kokkotou E., Dangond F. J. Biol. Chem. 280:28507-28518(2005) [PubMed: 15927959] [Abstract] Cited for: SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH HDAC1; HDAC2; HDAC3; RB1 AND HTLV-1 TAX.
[5]	"JMJD2A is a novel N-CoR-interacting protein and is involved in repression of the human transcription factor achaete scute-like homologue 2 (ASCL2/Hash2)." Zhang D., Yoon H.-G., Wong J. Mol. Cell. Biol. 25:6404-6414(2005) [PubMed: 16024779] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH NCOR1.
[6]	"Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry." Tao W.A., Wollscheid B., O'Brien R., Eng J.K., Li X.-J., Bodenmiller B., Watts J.D., Hood L., Aebersold R. Nat. Methods 2:591-598(2005) [PubMed: 16094384] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-547, MASS SPECTROMETRY. Tissue: T-cell.
[7]	"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases." Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y. Cell 125:467-481(2006) [PubMed: 16603238] [Abstract] Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, MUTAGENESIS OF HIS-188.
[8]	"Tudor, MBT and chromo domains gauge the degree of lysine methylation." Kim J., Daniel J., Espejo A., Lake A., Krishna M., Xia L., Zhang Y., Bedford M.T. EMBO Rep. 7:397-403(2006) [PubMed: 16415788] [Abstract] Cited for: DOMAIN.
[9]	"Structural insights into histone demethylation by JMJD2 family members." Chen Z., Zang J., Whetstine J., Hong X., Davrazou F., Kutateladze T.G., Simpson M., Mao Q., Pan C.-H., Dai S., Hagman J., Hansen K., Shi Y., Zhang G. Cell 125:691-702(2006) [PubMed: 16677698] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.28 ANGSTROMS) OF 1-350 IN COMPLEX WITH IRON AND ALPHA-KETOGLUTARATE, ZINC-BINDING, MUTAGENESIS OF GLY-133; GLY-138; GLY-165; GLY-170; 279-SER-THR-280 AND TYR-973.
[10]	"Recognition of histone H3 lysine-4 methylation by the double Tudor domain of JMJD2A." Huang Y., Fang J., Bedford M.T., Zhang Y., Xu R.-M. Science 312:748-751(2006) [PubMed: 16601153] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 895-1011 IN COMPLEX WITH TRIMETHYLATED H3 'LYS-4', DOMAIN, MUTAGENESIS OF ASP-945; TRP-967 AND TYR-973.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AB014577 mRNA. Translation: BAA31652.2. Different initiation.
AL451062, AC092815 Genomic DNA. Translation: CAH71021.1.
BC002558 mRNA. Translation: AAH02558.1.

IPI

IPI00005666.

RefSeq

NP_055478.2.

UniGene

Hs.155983

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2GF7	X-ray	2.20	A/B/C/D	895-1011	[»]
2GFA	X-ray	2.10	A/B	895-1011	[»]
2GP3	X-ray	2.35	A/B	2-350	[»]
2GP5	X-ray	2.28	A/B	2-350	[»]
2OQ6	X-ray	2.00	A/B	1-359	[»]
2OQ7	X-ray	2.15	A/B	1-359	[»]
2OS2	X-ray	2.30	A/B	1-359	[»]
2OT7	X-ray	2.13	A/B	1-359	[»]
2OX0	X-ray	1.95	A/B	1-359	[»]
2P5B	X-ray	1.99	A/B	2-350	[»]
2PXJ	X-ray	2.00	A/B	2-348	[»]
2Q8C	X-ray	2.05	A/B	1-350	[»]
2Q8D	X-ray	2.29	A/B	1-350	[»]
2Q8E	X-ray	2.05	A/B	1-350	[»]
2QQR	X-ray	1.80	A/B	897-1011	[»]
2QQS	X-ray	2.82	A/B	897-1011	[»]
2VD7	X-ray	2.25	A/B	1-359	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

O75164. 4 interactions.

STRING

O75164.

PTM databases

PhosphoSite

O75164.

Proteomic databases

PRIDE

O75164.

Genome annotation databases

Ensembl

ENST00000372396; ENSP00000361473; ENSG00000066135; Homo sapiens. [Genome view]

GeneID

9682.

KEGG

hsa:9682.

UCSC

uc001cjx.1. human.

Organism-specific databases

CTD

9682.

GeneCards

GC01P043888.

H-InvDB

HIX0020610.

HGNC

HGNC:22978. KDM4A.

HPA

HPA007610.

MIM

609764. gene.

PharmGKB

PA134971304.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

HOGENOM

O75164.

HOVERGEN

O75164.

Gene expression databases

ArrayExpress

O75164.

Bgee

O75164.

CleanEx

HS_JMJD2A.

Genevestigator

O75164.

GermOnline

ENSG00000066135. Homo sapiens.

Family and domain databases

InterPro

IPR013129. TF_JmjC.
IPR003347. TF_JmjC_AAH.
IPR003349. TF_JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
[Graphical view]

Pfam

PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]

SMART

SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]

PROSITE

PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS50304. TUDOR. False negative.
PS01359. ZF_PHD_1. False negative.
PS50016. ZF_PHD_2. False negative.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

36361.

SOURCE

Search...

Entry information

Entry name

KDM4A_HUMAN

Accession

Primary (citable) accession number: O75164
Secondary accession number(s): Q5VVB1

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 22, 2003
Last sequence update:	November 1, 1998
Last modified:	November 24, 2009
This is version 87 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.