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Lysine-specific demethylase 4A (EC 1.14.11.-) (JmjC domain-containing histone demethylation protein 3A) (Jumonji domain-containing protein 2A)

 KDM4A_HUMAN             Reviewed;        1064 AA.
O75164; Q5VVB1;
22-AUG-2003, integrated into UniProtKB/Swiss-Prot.
05-OCT-2010, sequence version 2.
22-NOV-2017, entry version 165.
RecName: Full=Lysine-specific demethylase 4A;
EC=1.14.11.-;
AltName: Full=JmjC domain-containing histone demethylation protein 3A;
AltName: Full=Jumonji domain-containing protein 2A;
Name=KDM4A; Synonyms=JHDM3A, JMJD2, JMJD2A, KIAA0677;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT
GLU-482.
TISSUE=Brain;
PubMed=9734811; DOI=10.1093/dnares/5.3.169;
Ishikawa K., Nagase T., Suyama M., Miyajima N., Tanaka A., Kotani H.,
Nomura N., Ohara O.;
"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.";
DNA Res. 5:169-176(1998).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16710414; DOI=10.1038/nature04727;
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.;
"The DNA sequence and biological annotation of human chromosome 1.";
Nature 441:315-321(2006).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), AND VARIANT
GLU-482.
TISSUE=Placenta;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[4]
SUBCELLULAR LOCATION, TISSUE SPECIFICITY, AND INTERACTION WITH HDAC1;
HDAC2; HDAC3; RB1 AND HTLV-1 TAX.
PubMed=15927959; DOI=10.1074/jbc.M413687200;
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.;
"Functional characterization of JMJD2A, a histone deacetylase- and
retinoblastoma-binding protein.";
J. Biol. Chem. 280:28507-28518(2005).
[5]
FUNCTION, SUBCELLULAR LOCATION, AND INTERACTION WITH NCOR1.
PubMed=16024779; DOI=10.1128/MCB.25.15.6404-6414.2005;
Zhang D., Yoon H.-G., Wong J.;
"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).";
Mol. Cell. Biol. 25:6404-6414(2005).
[6]
FUNCTION, CATALYTIC ACTIVITY, COFACTOR, DOMAIN, AND MUTAGENESIS OF
HIS-188.
PubMed=16603238; DOI=10.1016/j.cell.2006.03.028;
Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z.,
Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y.;
"Reversal of histone lysine trimethylation by the JMJD2 family of
histone demethylases.";
Cell 125:467-481(2006).
[7]
DOMAIN.
PubMed=16415788; DOI=10.1038/sj.embor.7400625;
Kim J., Daniel J., Espejo A., Lake A., Krishna M., Xia L., Zhang Y.,
Bedford M.T.;
"Tudor, MBT and chromo domains gauge the degree of lysine
methylation.";
EMBO Rep. 7:397-403(2006).
[8]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Cervix carcinoma;
PubMed=18669648; DOI=10.1073/pnas.0805139105;
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E.,
Elledge S.J., Gygi S.P.;
"A quantitative atlas of mitotic phosphorylation.";
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008).
[9]
ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS
SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19413330; DOI=10.1021/ac9004309;
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J.,
Mohammed S.;
"Lys-N and trypsin cover complementary parts of the phosphoproteome in
a refined SCX-based approach.";
Anal. Chem. 81:4493-4501(2009).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=21406692; DOI=10.1126/scisignal.2001570;
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J.,
Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V.,
Blagoev B.;
"System-wide temporal characterization of the proteome and
phosphoproteome of human embryonic stem cell differentiation.";
Sci. Signal. 4:RS3-RS3(2011).
[11]
UBIQUITINATION, DOMAIN, AND MUTAGENESIS OF HIS-188 AND ASP-939.
PubMed=22373579; DOI=10.1038/emboj.2012.47;
Mallette F.A., Mattiroli F., Cui G., Young L.C., Hendzel M.J., Mer G.,
Sixma T.K., Richard S.;
"RNF8- and RNF168-dependent degradation of KDM4A/JMJD2A triggers 53BP1
recruitment to DNA damage sites.";
EMBO J. 31:1865-1878(2012).
[12]
ALTERNATIVE SPLICING (ISOFORM 2), AND FUNCTION (ISOFORM 2).
PubMed=21694756; DOI=10.1371/journal.pgen.1001390;
Verrier L., Escaffit F., Chailleux C., Trouche D., Vandromme M.;
"A new isoform of the histone demethylase JMJD2A/KDM4A is required for
skeletal muscle differentiation.";
PLoS Genet. 7:E1001390-E1001390(2011).
[13]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-523, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Erythroleukemia;
PubMed=23186163; DOI=10.1021/pr300630k;
Zhou H., Di Palma S., Preisinger C., Peng M., Polat A.N., Heck A.J.,
Mohammed S.;
"Toward a comprehensive characterization of a human cancer cell
phosphoproteome.";
J. Proteome Res. 12:260-271(2013).
[14]
X-RAY CRYSTALLOGRAPHY (2.28 ANGSTROMS) OF 1-350 IN COMPLEX WITH IRON
AND 2-OXOGLUTARATE, ZINC-BINDING, AND MUTAGENESIS OF GLY-133; GLY-138;
GLY-165; GLY-170; 279-SER-THR-280 AND TYR-973.
PubMed=16677698; DOI=10.1016/j.cell.2006.04.024;
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.;
"Structural insights into histone demethylation by JMJD2 family
members.";
Cell 125:691-702(2006).
[15]
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 895-1011 IN COMPLEX WITH
TRIMETHYLATED H3 'LYS-4', DOMAIN, AND MUTAGENESIS OF ASP-945; TRP-967
AND TYR-973.
PubMed=16601153; DOI=10.1126/science.1125162;
Huang Y., Fang J., Bedford M.T., Zhang Y., Xu R.-M.;
"Recognition of histone H3 lysine-4 methylation by the double Tudor
domain of JMJD2A.";
Science 312:748-751(2006).
[16]
X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) OF 4-355 IN COMPLEX WITH ZINC
AND SEVERAL INHIBITORS, FUNCTION, ENZYME REGULATION, AND COFACTOR.
PubMed=26741168; DOI=10.1021/ACS.JMEDCHEM.5B01635;
Bavetsias V., Lanigan R.M., Ruda G.F., Atrash B., McLaughlin M.G.,
Tumber A., Mok N.Y., Le Bihan Y.V., Dempster S., Boxall K.J.,
Jeganathan F., Hatch S.B., Savitsky P., Velupillai S., Krojer T.,
England K.S., Sejberg J., Thai C., Donovan A., Pal A., Scozzafava G.,
Bennett J.M., Kawamura A., Johansson C., Szykowska A., Gileadi C.,
Burgess-Brown N.A., von Delft F., Oppermann U., Walters Z.,
Shipley J., Raynaud F.I., Westaway S.M., Prinjha R.K., Fedorov O.,
Burke R., Schofield C.J., Westwood I.M., Bountra C., Muller S.,
van Montfort R.L., Brennan P.E., Blagg J.;
"8-Substituted Pyrido[3,4-d]pyrimidin-4(3H)-one Derivatives As Potent,
Cell Permeable, KDM4 (JMJD2) and KDM5 (JARID1) Histone Lysine
Demethylase Inhibitors.";
J. Med. Chem. 59:1388-1409(2016).
[17]
X-RAY CRYSTALLOGRAPHY (2.44 ANGSTROMS) OF 11-161 AND 170-354.
PubMed=27214403; DOI=10.1038/NCHEMBIO.2087;
Johansson C., Velupillai S., Tumber A., Szykowska A., Hookway E.S.,
Nowak R.P., Strain-Damerell C., Gileadi C., Philpott M.,
Burgess-Brown N., Wu N., Kopec J., Nuzzi A., Steuber H., Egner U.,
Badock V., Munro S., LaThangue N.B., Westaway S., Brown J.,
Athanasou N., Prinjha R., Brennan P.E., Oppermann U.;
"Structural analysis of human KDM5B guides histone demethylase
inhibitor development.";
Nat. Chem. Biol. 12:539-545(2016).
-!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-
9' and 'Lys-36' residues of histone H3, thereby playing a central
role in histone code (PubMed:26741168). 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. {ECO:0000269|PubMed:26741168}.
-!- FUNCTION: Isoform 2: Crucial for muscle differentiation, promotes
transcriptional activation of the Myog gene by directing the
removal of repressive chromatin marks at its promoter. Lacks the
N-terminal demethylase domain.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
Evidence={ECO:0000269|PubMed:16603238};
Note=Binds 1 Fe(2+) ion per subunit.
{ECO:0000269|PubMed:16603238};
-!- ENZYME REGULATION: Several specific inhibitors are being developed
and tested. {ECO:0000269|PubMed:26741168}.
-!- SUBUNIT: Interacts with histone deacetylase proteins HDAC1, HDAC2
and HDAC3. Interacts with RB and NCOR1. Interacts with HTLV-1 Tax
protein. {ECO:0000269|PubMed:15927959,
ECO:0000269|PubMed:16024779, ECO:0000269|PubMed:16601153,
ECO:0000269|PubMed:16677698}.
-!- INTERACTION:
P68431:HIST1H3D; NbExp=7; IntAct=EBI-936709, EBI-79722;
P62805:HIST2H4B; NbExp=7; IntAct=EBI-936709, EBI-302023;
Q16695:HIST3H3; NbExp=6; IntAct=EBI-936709, EBI-358900;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00537, ECO:0000269|PubMed:15927959,
ECO:0000269|PubMed:16024779}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=O75164-1; Sequence=Displayed;
Name=2; Synonyms=deltaN-JMJD2A;
IsoId=O75164-2; Sequence=VSP_044239;
-!- TISSUE SPECIFICITY: Ubiquitous. {ECO:0000269|PubMed:15927959}.
-!- DOMAIN: The 2 Tudor domains recognize and bind methylated histone
H3 'Lys-4' residue (H3K4me). 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'
(H3K4me3) 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 also able to bind
trimethylated histone H3 'Lys-9' (H3K9me3), di- and trimethylated
H4 'Lys-20' (H4K20me2 and H4K20me3). Has high affinity for
H4K20me2, blocking recruitment of proteins such as TP53BP1.
{ECO:0000269|PubMed:16415788, ECO:0000269|PubMed:16601153,
ECO:0000269|PubMed:16603238, ECO:0000269|PubMed:22373579}.
-!- PTM: Ubiquitinated by RNF8 and RNF168 following DNA damage,
leading to its degradation. Degradation promotes accessibility of
H4K20me2 mark for DNA repair protein TP53BP1, which is then
recruited. {ECO:0000269|PubMed:22373579}.
-!- SIMILARITY: Belongs to the JHDM3 histone demethylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAA31652.2; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; AB014577; BAA31652.2; ALT_INIT; mRNA.
EMBL; AL451062; CAH71021.1; -; Genomic_DNA.
EMBL; AC092815; CAH71021.1; JOINED; Genomic_DNA.
EMBL; BC002558; AAH02558.1; -; mRNA.
CCDS; CCDS491.1; -. [O75164-1]
RefSeq; NP_055478.2; NM_014663.2. [O75164-1]
RefSeq; XP_005271411.1; XM_005271354.3. [O75164-1]
RefSeq; XP_005271412.1; XM_005271355.3. [O75164-1]
UniGene; Hs.155983; -.
PDB; 2GF7; X-ray; 2.20 A; A/B/C/D=895-1011.
PDB; 2GFA; X-ray; 2.10 A; A/B=895-1011.
PDB; 2GP3; X-ray; 2.35 A; A/B=2-350.
PDB; 2GP5; X-ray; 2.28 A; A/B=2-350.
PDB; 2OQ6; X-ray; 2.00 A; A/B=1-359.
PDB; 2OQ7; X-ray; 2.15 A; A/B=1-359.
PDB; 2OS2; X-ray; 2.30 A; A/B=1-359.
PDB; 2OT7; X-ray; 2.13 A; A/B=1-359.
PDB; 2OX0; X-ray; 1.95 A; A/B=1-359.
PDB; 2P5B; X-ray; 1.99 A; A/B=2-350.
PDB; 2PXJ; X-ray; 2.00 A; A/B=2-348.
PDB; 2Q8C; X-ray; 2.05 A; A/B=1-350.
PDB; 2Q8D; X-ray; 2.29 A; A/B=1-350.
PDB; 2Q8E; X-ray; 2.05 A; A/B=1-350.
PDB; 2QQR; X-ray; 1.80 A; A/B=897-1011.
PDB; 2QQS; X-ray; 2.82 A; A/B=897-1011.
PDB; 2VD7; X-ray; 2.25 A; A/B=1-359.
PDB; 2WWJ; X-ray; 2.60 A; A/B=7-353.
PDB; 2YBK; X-ray; 2.40 A; A/B=1-359.
PDB; 2YBP; X-ray; 2.02 A; A/B=1-359.
PDB; 2YBS; X-ray; 2.32 A; A/B=1-359.
PDB; 3NJY; X-ray; 2.60 A; A/B=1-359.
PDB; 3PDQ; X-ray; 1.99 A; A/B=1-359.
PDB; 3RVH; X-ray; 2.25 A; A/B=1-359.
PDB; 3U4S; X-ray; 2.15 A; A/B=1-359.
PDB; 4AI9; X-ray; 2.25 A; A/B=1-359.
PDB; 4BIS; X-ray; 2.49 A; A/B=1-359.
PDB; 4GD4; X-ray; 2.33 A; A/B=1-359.
PDB; 4URA; X-ray; 2.23 A; A/B=1-359.
PDB; 4V2V; X-ray; 2.00 A; A/B=1-359.
PDB; 4V2W; X-ray; 1.81 A; A/B=1-359.
PDB; 5A7N; X-ray; 2.39 A; A/B=1-359.
PDB; 5A7O; X-ray; 2.15 A; A/B=1-359.
PDB; 5A7P; X-ray; 2.28 A; A/B=1-359.
PDB; 5A7Q; X-ray; 2.00 A; A/B=1-359.
PDB; 5A7S; X-ray; 2.20 A; A/B=1-359.
PDB; 5A7W; X-ray; 2.27 A; A/B=1-359.
PDB; 5A80; X-ray; 2.28 A; A/B=1-359.
PDB; 5ANQ; X-ray; 2.00 A; A/B=1-359.
PDB; 5D6W; X-ray; 1.99 A; A/B/C/D=895-1011.
PDB; 5D6X; X-ray; 2.15 A; A/B=895-1011.
PDB; 5D6Y; X-ray; 2.29 A; A/B/C/D/E/F=895-1011.
PDB; 5F2S; X-ray; 2.08 A; A/B/C/D=1-359.
PDB; 5F2W; X-ray; 2.60 A; A/B/C/D=1-359.
PDB; 5F32; X-ray; 2.05 A; A/B/C/D=1-359.
PDB; 5F37; X-ray; 2.22 A; A/B/C/D=1-359.
PDB; 5F39; X-ray; 2.65 A; A/B/C/D=1-359.
PDB; 5F3C; X-ray; 2.06 A; A/B/C/D=1-359.
PDB; 5F3E; X-ray; 2.16 A; A/B/C/D=1-359.
PDB; 5F3G; X-ray; 2.50 A; A/B/C/D=1-359.
PDB; 5F3I; X-ray; 2.24 A; A/B/C/D=1-359.
PDB; 5F5I; X-ray; 2.63 A; A/B=1-359.
PDB; 5FPV; X-ray; 2.44 A; A/B/C/D/E/F/G/H=1-359.
PDB; 5FWE; X-ray; 2.05 A; A/B=1-359.
PDB; 5FY8; X-ray; 2.34 A; A/B=1-359.
PDB; 5FYC; X-ray; 2.26 A; A/B=1-359.
PDB; 5FYH; X-ray; 2.35 A; A/B=1-359.
PDB; 5FYI; X-ray; 2.10 A; A/B=1-359.
PDB; 5LY1; X-ray; 2.50 A; A/B/C/D=1-359.
PDB; 5LY2; X-ray; 2.43 A; A/B/C/D=1-359.
PDB; 5TVR; X-ray; 2.09 A; A/B=1-359.
PDB; 5TVS; X-ray; 2.75 A; A/B=1-359.
PDB; 5VGI; X-ray; 2.07 A; A/B/C/D=5-354.
PDB; 5VMP; X-ray; 2.48 A; A/B/C/D=5-354.
PDBsum; 2GF7; -.
PDBsum; 2GFA; -.
PDBsum; 2GP3; -.
PDBsum; 2GP5; -.
PDBsum; 2OQ6; -.
PDBsum; 2OQ7; -.
PDBsum; 2OS2; -.
PDBsum; 2OT7; -.
PDBsum; 2OX0; -.
PDBsum; 2P5B; -.
PDBsum; 2PXJ; -.
PDBsum; 2Q8C; -.
PDBsum; 2Q8D; -.
PDBsum; 2Q8E; -.
PDBsum; 2QQR; -.
PDBsum; 2QQS; -.
PDBsum; 2VD7; -.
PDBsum; 2WWJ; -.
PDBsum; 2YBK; -.
PDBsum; 2YBP; -.
PDBsum; 2YBS; -.
PDBsum; 3NJY; -.
PDBsum; 3PDQ; -.
PDBsum; 3RVH; -.
PDBsum; 3U4S; -.
PDBsum; 4AI9; -.
PDBsum; 4BIS; -.
PDBsum; 4GD4; -.
PDBsum; 4URA; -.
PDBsum; 4V2V; -.
PDBsum; 4V2W; -.
PDBsum; 5A7N; -.
PDBsum; 5A7O; -.
PDBsum; 5A7P; -.
PDBsum; 5A7Q; -.
PDBsum; 5A7S; -.
PDBsum; 5A7W; -.
PDBsum; 5A80; -.
PDBsum; 5ANQ; -.
PDBsum; 5D6W; -.
PDBsum; 5D6X; -.
PDBsum; 5D6Y; -.
PDBsum; 5F2S; -.
PDBsum; 5F2W; -.
PDBsum; 5F32; -.
PDBsum; 5F37; -.
PDBsum; 5F39; -.
PDBsum; 5F3C; -.
PDBsum; 5F3E; -.
PDBsum; 5F3G; -.
PDBsum; 5F3I; -.
PDBsum; 5F5I; -.
PDBsum; 5FPV; -.
PDBsum; 5FWE; -.
PDBsum; 5FY8; -.
PDBsum; 5FYC; -.
PDBsum; 5FYH; -.
PDBsum; 5FYI; -.
PDBsum; 5LY1; -.
PDBsum; 5LY2; -.
PDBsum; 5TVR; -.
PDBsum; 5TVS; -.
PDBsum; 5VGI; -.
PDBsum; 5VMP; -.
ProteinModelPortal; O75164; -.
SMR; O75164; -.
BioGrid; 115035; 29.
CORUM; O75164; -.
DIP; DIP-29372N; -.
IntAct; O75164; 28.
MINT; MINT-2829088; -.
STRING; 9606.ENSP00000361473; -.
BindingDB; O75164; -.
ChEMBL; CHEMBL5896; -.
GuidetoPHARMACOLOGY; 2675; -.
iPTMnet; O75164; -.
PhosphoSitePlus; O75164; -.
BioMuta; KDM4A; -.
EPD; O75164; -.
MaxQB; O75164; -.
PaxDb; O75164; -.
PeptideAtlas; O75164; -.
PRIDE; O75164; -.
Ensembl; ENST00000372396; ENSP00000361473; ENSG00000066135. [O75164-1]
GeneID; 9682; -.
KEGG; hsa:9682; -.
UCSC; uc001cjx.4; human. [O75164-1]
CTD; 9682; -.
DisGeNET; 9682; -.
EuPathDB; HostDB:ENSG00000066135.12; -.
GeneCards; KDM4A; -.
H-InvDB; HIX0020610; -.
HGNC; HGNC:22978; KDM4A.
HPA; HPA007610; -.
MIM; 609764; gene.
neXtProt; NX_O75164; -.
OpenTargets; ENSG00000066135; -.
PharmGKB; PA164721403; -.
eggNOG; ENOG410IT40; Eukaryota.
eggNOG; COG5141; LUCA.
GeneTree; ENSGT00530000063342; -.
HOGENOM; HOG000231125; -.
InParanoid; O75164; -.
KO; K06709; -.
OMA; CRAQGQT; -.
OrthoDB; EOG091G01FR; -.
PhylomeDB; O75164; -.
TreeFam; TF106449; -.
BRENDA; 1.14.11.27; 2681.
BRENDA; 1.14.11.B1; 2681.
BRENDA; 1.14.11.B2; 2681.
Reactome; R-HSA-3214842; HDMs demethylate histones.
Reactome; R-HSA-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
ChiTaRS; KDM4A; human.
EvolutionaryTrace; O75164; -.
GeneWiki; JMJD2A; -.
GenomeRNAi; 9682; -.
PRO; PR:O75164; -.
Proteomes; UP000005640; Chromosome 1.
Bgee; ENSG00000066135; -.
CleanEx; HS_JMJD2A; -.
Genevisible; O75164; HS.
GO; GO:0005829; C:cytosol; IDA:HPA.
GO; GO:0001650; C:fibrillar center; IDA:HPA.
GO; GO:0005654; C:nucleoplasm; TAS:Reactome.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0005721; C:pericentric heterochromatin; IEA:Ensembl.
GO; GO:0032452; F:histone demethylase activity; TAS:Reactome.
GO; GO:0051864; F:histone demethylase activity (H3-K36 specific); IDA:UniProtKB.
GO; GO:0032454; F:histone demethylase activity (H3-K9 specific); IMP:UniProtKB.
GO; GO:0035064; F:methylated histone binding; IDA:UniProtKB.
GO; GO:0031625; F:ubiquitin protein ligase binding; IPI:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
GO; GO:0014898; P:cardiac muscle hypertrophy in response to stress; IEA:Ensembl.
GO; GO:0016577; P:histone demethylation; IDA:UniProtKB.
GO; GO:0070544; P:histone H3-K36 demethylation; IDA:UniProtKB.
GO; GO:0033169; P:histone H3-K9 demethylation; IMP:UniProtKB.
GO; GO:0048712; P:negative regulation of astrocyte differentiation; IEA:Ensembl.
GO; GO:0010507; P:negative regulation of autophagy; IMP:ParkinsonsUK-UCL.
GO; GO:0060548; P:negative regulation of cell death; IEA:Ensembl.
GO; GO:0010629; P:negative regulation of gene expression; IMP:ParkinsonsUK-UCL.
GO; GO:1900113; P:negative regulation of histone H3-K9 trimethylation; IEA:Ensembl.
GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IDA:UniProtKB.
GO; GO:0010628; P:positive regulation of gene expression; IEA:Ensembl.
GO; GO:0045666; P:positive regulation of neuron differentiation; IEA:Ensembl.
GO; GO:0031667; P:response to nutrient levels; IEA:Ensembl.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0016032; P:viral process; IEA:UniProtKB-KW.
Gene3D; 3.30.40.10; -; 3.
InterPro; IPR034732; EPHD.
InterPro; IPR003347; JmjC_dom.
InterPro; IPR003349; JmjN.
InterPro; IPR002999; Tudor.
InterPro; IPR011011; Znf_FYVE_PHD.
InterPro; IPR001965; Znf_PHD.
InterPro; IPR013083; Znf_RING/FYVE/PHD.
Pfam; PF02373; JmjC; 1.
Pfam; PF02375; JmjN; 1.
SMART; SM00558; JmjC; 1.
SMART; SM00545; JmjN; 1.
SMART; SM00249; PHD; 2.
SMART; SM00333; TUDOR; 2.
SUPFAM; SSF57903; SSF57903; 1.
PROSITE; PS51805; EPHD; 1.
PROSITE; PS51184; JMJC; 1.
PROSITE; PS51183; JMJN; 1.
1: Evidence at protein level;
3D-structure; Acetylation; Alternative splicing; Chromatin regulator;
Complete proteome; Dioxygenase; Host-virus interaction; Iron;
Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein; Polymorphism;
Reference proteome; Repeat; Transcription; Transcription regulation;
Ubl conjugation; Zinc; Zinc-finger.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:19413330}.
CHAIN 2 1064 Lysine-specific demethylase 4A.
/FTId=PRO_0000183172.
DOMAIN 14 56 JmjN. {ECO:0000255|PROSITE-
ProRule:PRU00537}.
DOMAIN 142 308 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
DOMAIN 897 954 Tudor 1.
DOMAIN 955 1011 Tudor 2.
ZN_FING 709 767 PHD-type 1.
ZN_FING 772 805 C2HC pre-PHD-type. {ECO:0000255|PROSITE-
ProRule:PRU01146}.
ZN_FING 828 885 PHD-type 2. {ECO:0000255|PROSITE-
ProRule:PRU01146}.
REGION 597 638 Interaction with NCOR1.
{ECO:0000269|PubMed:16024779}.
METAL 188 188 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538,
ECO:0000269|PubMed:16677698,
ECO:0000305|PubMed:26741168}.
METAL 190 190 Iron; catalytic.
{ECO:0000269|PubMed:16677698,
ECO:0000305|PubMed:26741168}.
METAL 234 234 Zinc. {ECO:0000244|PDB:5F2W,
ECO:0000244|PDB:5F32,
ECO:0000244|PDB:5F37,
ECO:0000244|PDB:5F39,
ECO:0000244|PDB:5F3E,
ECO:0000244|PDB:5F3G,
ECO:0000244|PDB:5F5I}.
METAL 240 240 Zinc; via tele nitrogen.
{ECO:0000244|PDB:5F2W,
ECO:0000244|PDB:5F32,
ECO:0000244|PDB:5F37,
ECO:0000244|PDB:5F39,
ECO:0000244|PDB:5F3E,
ECO:0000244|PDB:5F3G,
ECO:0000244|PDB:5F5I}.
METAL 276 276 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538,
ECO:0000269|PubMed:16677698,
ECO:0000305|PubMed:26741168}.
METAL 306 306 Zinc. {ECO:0000244|PDB:5F2W,
ECO:0000244|PDB:5F32,
ECO:0000244|PDB:5F37,
ECO:0000244|PDB:5F39,
ECO:0000244|PDB:5F3E,
ECO:0000244|PDB:5F3G,
ECO:0000244|PDB:5F5I}.
METAL 308 308 Zinc. {ECO:0000244|PDB:5F2W,
ECO:0000244|PDB:5F32,
ECO:0000244|PDB:5F37,
ECO:0000244|PDB:5F39,
ECO:0000244|PDB:5F3E,
ECO:0000244|PDB:5F3G,
ECO:0000244|PDB:5F5I}.
BINDING 132 132 2-oxoglutarate.
{ECO:0000269|PubMed:16677698}.
BINDING 198 198 2-oxoglutarate.
{ECO:0000269|PubMed:16677698}.
BINDING 206 206 2-oxoglutarate.
{ECO:0000269|PubMed:16677698}.
BINDING 241 241 2-oxoglutarate.
{ECO:0000250|UniProtKB:B2RXH2}.
BINDING 945 945 Histone H3K4me3.
BINDING 967 967 Histone H3K4me3.
BINDING 973 973 Histone H3K4me3.
MOD_RES 2 2 N-acetylalanine.
{ECO:0000244|PubMed:19413330}.
MOD_RES 523 523 Phosphoserine.
{ECO:0000244|PubMed:23186163}.
VAR_SEQ 1 583 Missing (in isoform 2). {ECO:0000305}.
/FTId=VSP_044239.
VARIANT 482 482 A -> E (in dbSNP:rs586339).
{ECO:0000269|PubMed:15489334,
ECO:0000269|PubMed:9734811}.
/FTId=VAR_023775.
VARIANT 877 877 V -> G (in dbSNP:rs12759032).
/FTId=VAR_031217.
MUTAGEN 133 133 G->A: Abolishes histone demethylase
activity; when associated with A-138.
{ECO:0000269|PubMed:16677698}.
MUTAGEN 138 138 G->A: Abolishes histone demethylase
activity; when associated with A-138.
{ECO:0000269|PubMed:16677698}.
MUTAGEN 165 165 G->A: Abolishes histone demethylase
activity; when associated with A-165.
{ECO:0000269|PubMed:16677698}.
MUTAGEN 170 170 G->A: Abolishes histone demethylase
activity; when associated with A-165.
{ECO:0000269|PubMed:16677698}.
MUTAGEN 188 188 H->A: Abolishes histone demethylase
activity without affecting ability to
bind H4K20me2.
{ECO:0000269|PubMed:16603238,
ECO:0000269|PubMed:22373579}.
MUTAGEN 288 289 ST->AI: Displays histone demethylase
activity for both dimethylated and H3-
K9Me3.
MUTAGEN 288 289 ST->TV,NV,GG: Abolishes histone
demethylase activity.
MUTAGEN 939 939 D->R: Impairs binding to H4K20me2,
promoting partial recruitment of TP53BP1.
{ECO:0000269|PubMed:22373579}.
MUTAGEN 945 945 D->A: Impairs binding to H3K4me3.
{ECO:0000269|PubMed:16601153}.
MUTAGEN 945 945 D->R: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:16601153}.
MUTAGEN 967 967 W->H: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:16601153}.
MUTAGEN 973 973 Y->A: Abolishes binding to H3K4me3.
{ECO:0000269|PubMed:16601153,
ECO:0000269|PubMed:16677698}.
TURN 4 6 {ECO:0000244|PDB:4V2W}.
STRAND 7 9 {ECO:0000244|PDB:5A7S}.
HELIX 10 12 {ECO:0000244|PDB:5A7W}.
STRAND 15 17 {ECO:0000244|PDB:4V2W}.
HELIX 21 24 {ECO:0000244|PDB:4V2W}.
HELIX 27 36 {ECO:0000244|PDB:4V2W}.
HELIX 39 42 {ECO:0000244|PDB:4V2W}.
STRAND 43 47 {ECO:0000244|PDB:4V2W}.
STRAND 55 57 {ECO:0000244|PDB:5A7W}.
STRAND 59 61 {ECO:0000244|PDB:3PDQ}.
HELIX 62 64 {ECO:0000244|PDB:5A7Q}.
STRAND 66 69 {ECO:0000244|PDB:4V2W}.
STRAND 71 78 {ECO:0000244|PDB:4V2W}.
STRAND 81 88 {ECO:0000244|PDB:4V2W}.
HELIX 94 101 {ECO:0000244|PDB:4V2W}.
TURN 104 106 {ECO:0000244|PDB:4V2W}.
HELIX 114 124 {ECO:0000244|PDB:4V2W}.
STRAND 131 137 {ECO:0000244|PDB:4V2W}.
HELIX 150 152 {ECO:0000244|PDB:5F32}.
HELIX 156 158 {ECO:0000244|PDB:4V2W}.
HELIX 159 162 {ECO:0000244|PDB:4V2W}.
STRAND 163 165 {ECO:0000244|PDB:5A7W}.
TURN 169 171 {ECO:0000244|PDB:3PDQ}.
STRAND 175 179 {ECO:0000244|PDB:4V2W}.
STRAND 184 188 {ECO:0000244|PDB:4V2W}.
HELIX 191 193 {ECO:0000244|PDB:4V2W}.
STRAND 195 204 {ECO:0000244|PDB:4V2W}.
STRAND 206 211 {ECO:0000244|PDB:4V2W}.
HELIX 213 215 {ECO:0000244|PDB:4V2W}.
HELIX 216 226 {ECO:0000244|PDB:4V2W}.
HELIX 228 233 {ECO:0000244|PDB:4V2W}.
HELIX 237 240 {ECO:0000244|PDB:4V2W}.
STRAND 243 245 {ECO:0000244|PDB:4V2W}.
HELIX 247 252 {ECO:0000244|PDB:4V2W}.
STRAND 258 262 {ECO:0000244|PDB:4V2W}.
STRAND 267 270 {ECO:0000244|PDB:4V2W}.
STRAND 275 280 {ECO:0000244|PDB:4V2W}.
STRAND 282 291 {ECO:0000244|PDB:4V2W}.
HELIX 296 302 {ECO:0000244|PDB:4V2W}.
STRAND 308 311 {ECO:0000244|PDB:2P5B}.
HELIX 318 324 {ECO:0000244|PDB:4V2W}.
HELIX 326 333 {ECO:0000244|PDB:4V2W}.
STRAND 343 345 {ECO:0000244|PDB:5F3I}.
HELIX 348 353 {ECO:0000244|PDB:4V2W}.
STRAND 904 908 {ECO:0000244|PDB:2QQR}.
STRAND 912 932 {ECO:0000244|PDB:2QQR}.
STRAND 937 941 {ECO:0000244|PDB:2QQR}.
HELIX 943 945 {ECO:0000244|PDB:2QQR}.
HELIX 951 954 {ECO:0000244|PDB:2QQR}.
STRAND 962 966 {ECO:0000244|PDB:2QQR}.
STRAND 972 990 {ECO:0000244|PDB:2QQR}.
STRAND 995 998 {ECO:0000244|PDB:2QQR}.
HELIX 1000 1002 {ECO:0000244|PDB:2QQR}.
STRAND 1003 1005 {ECO:0000244|PDB:2QQR}.
SEQUENCE 1064 AA; 120662 MW; 4A811BEECFEDC6B3 CRC64;
MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP KEWKPRASYD
DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI ANSDKYCTPR YSEFEELERK
YWKNLTFNPP IYGADVNGTL YEKHVDEWNI GRLRTILDLV EKESGITIEG VNTPYLYFGM
WKTSFAWHTE DMDLYSINYL HFGEPKSWYS VPPEHGKRLE RLAKGFFPGS AQSCEAFLRH
KMTLISPLML KKYGIPFDKV TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATRRWIEYG
KQAVLCSCRK DMVKISMDVF VRKFQPERYK LWKAGKDNTV IDHTLPTPEA AEFLKESELP
PRAGNEEECP EEDMEGVEDG EEGDLKTSLA KHRIGTKRHR VCLEIPQEVS QSELFPKEDL
SSEQYEMTEC PAALAPVRPT HSSVRQVEDG LTFPDYSDST EVKFEELKNV KLEEEDEEEE
QAAAALDLSV NPASVGGRLV FSGSKKKSSS SLGSGSSRDS ISSDSETSEP LSCRAQGQTG
VLTVHSYAKG DGRVTVGEPC TRKKGSAARS FSERELAEVA DEYMFSLEEN KKSKGRRQPL
SKLPRHHPLV LQECVSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN FEAEKEFNET
MAQQAPHCAV CMIFQTYHQV EFGGFNQNCG NASDLAPQKQ RTKPLIPEMC FTSTGCSTDI
NLSTPYLEED GTSILVSCKK CSVRVHASCY GVPPAKASED WMCSRCSANA LEEDCCLCSL
RGGALQRAND DRWVHVSCAV AILEARFVNI AERSPVDVSK IPLPRFKLKC IFCKKRRKRT
AGCCVQCSHG RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALQSIT
AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD CLQFGPPAEG
EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR DDVYTLDEEL PKRVKSRLSV
ASDMRFNEIF TEKEVKQEKK RQRVINSRYR EDYIEPALYR AIME


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