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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_MOUSE             Reviewed;        1064 AA.
Q8BW72; A2A8L8; Q3UKM5; Q3UM81; Q3UWV2; Q6ZQ72; Q8K137;
16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 3.
27-SEP-2017, entry version 131.
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;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Embryonic tail;
PubMed=14621295; DOI=10.1093/dnares/10.4.167;
Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S.,
Saga Y., Nagase T., Ohara O., Koga H.;
"Prediction of the coding sequences of mouse homologues of KIAA gene:
III. The complete nucleotide sequences of 500 mouse KIAA-homologous
cDNAs identified by screening of terminal sequences of cDNA clones
randomly sampled from size-fractionated libraries.";
DNA Res. 10:167-180(2003).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=C57BL/6J; TISSUE=Embryo, Mammary gland, Oviduct, and Placenta;
PubMed=16141072; DOI=10.1126/science.1112014;
Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N.,
Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K.,
Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M.,
Davis M.J., Wilming L.G., Aidinis V., Allen J.E.,
Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L.,
Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M.,
Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R.,
Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G.,
di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G.,
Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M.,
Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E.,
Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N.,
Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T.,
Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H.,
Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K.,
Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J.,
Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L.,
Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K.,
Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P.,
Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O.,
Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G.,
Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M.,
Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C.,
Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y.,
Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B.,
Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K.,
Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A.,
Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K.,
Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C.,
Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J.,
Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y.,
Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T.,
Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N.,
Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N.,
Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S.,
Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J.,
Hayashizaki Y.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
STRAIN=FVB/N; TISSUE=Colon;
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).
[5]
PROTEIN SEQUENCE OF 499-505, AND IDENTIFICATION BY MASS SPECTROMETRY.
STRAIN=OF1; TISSUE=Hippocampus;
Lubec G., Sunyer B., Chen W.-Q.;
Submitted (JAN-2009) to UniProtKB.
[6]
TISSUE SPECIFICITY.
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).
-!- 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 (By
similarity). {ECO:0000250}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBUNIT: Interacts with histone deacetylase proteins HDAC1, HDAC2
and HDAC3. Interacts with RB and NCOR1 (By similarity).
{ECO:0000250}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-
ProRule:PRU00537}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q8BW72-1; Sequence=Displayed;
Name=2;
IsoId=Q8BW72-2; Sequence=VSP_016144, VSP_016145;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Widely expressed.
{ECO:0000269|PubMed:16024779}.
-!- 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 (By
similarity). {ECO:0000250}.
-!- 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 (By similarity). {ECO:0000250}.
-!- SIMILARITY: Belongs to the JHDM3 histone demethylase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAC97997.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};
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EMBL; AK129187; BAC97997.1; ALT_INIT; mRNA.
EMBL; AK054095; BAC35653.1; -; mRNA.
EMBL; AK136085; BAE22812.1; -; mRNA.
EMBL; AK145066; BAE26217.1; -; mRNA.
EMBL; AK145947; BAE26776.1; -; mRNA.
EMBL; AL626764; CAM27385.1; -; Genomic_DNA.
EMBL; BC028866; AAH28866.1; -; mRNA.
CCDS; CCDS51282.1; -. [Q8BW72-1]
RefSeq; NP_001155295.1; NM_001161823.1. [Q8BW72-1]
RefSeq; NP_759014.2; NM_172382.2.
RefSeq; XP_006503073.1; XM_006503010.2. [Q8BW72-1]
UniGene; Mm.234234; -.
ProteinModelPortal; Q8BW72; -.
SMR; Q8BW72; -.
BioGrid; 230999; 4.
IntAct; Q8BW72; 1.
STRING; 10090.ENSMUSP00000095524; -.
iPTMnet; Q8BW72; -.
PhosphoSitePlus; Q8BW72; -.
EPD; Q8BW72; -.
PaxDb; Q8BW72; -.
PeptideAtlas; Q8BW72; -.
PRIDE; Q8BW72; -.
Ensembl; ENSMUST00000097911; ENSMUSP00000095524; ENSMUSG00000033326. [Q8BW72-1]
Ensembl; ENSMUST00000106403; ENSMUSP00000102011; ENSMUSG00000033326. [Q8BW72-1]
Ensembl; ENSMUST00000106406; ENSMUSP00000102014; ENSMUSG00000033326. [Q8BW72-1]
GeneID; 230674; -.
KEGG; mmu:230674; -.
UCSC; uc008ujn.2; mouse. [Q8BW72-1]
CTD; 9682; -.
MGI; MGI:2446210; Kdm4a.
eggNOG; ENOG410IT40; Eukaryota.
eggNOG; COG5141; LUCA.
GeneTree; ENSGT00530000063342; -.
HOVERGEN; HBG080483; -.
InParanoid; Q8BW72; -.
KO; K06709; -.
OMA; CRAQGQT; -.
OrthoDB; EOG091G01FR; -.
TreeFam; TF106449; -.
Reactome; R-MMU-3214842; HDMs demethylate histones.
Reactome; R-MMU-5693565; Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks.
ChiTaRS; Kdm4a; mouse.
PRO; PR:Q8BW72; -.
Proteomes; UP000000589; Chromosome 4.
Bgee; ENSMUSG00000033326; -.
CleanEx; MM_JMJD2A; -.
ExpressionAtlas; Q8BW72; baseline and differential.
Genevisible; Q8BW72; MM.
GO; GO:0005829; C:cytosol; ISO:MGI.
GO; GO:0001650; C:fibrillar center; ISO:MGI.
GO; GO:0005634; C:nucleus; ISO:MGI.
GO; GO:0005721; C:pericentric heterochromatin; IDA:MGI.
GO; GO:0032452; F:histone demethylase activity; IDA:MGI.
GO; GO:0051864; F:histone demethylase activity (H3-K36 specific); ISO:MGI.
GO; GO:0032454; F:histone demethylase activity (H3-K9 specific); ISO:MGI.
GO; GO:0035064; F:methylated histone binding; ISS:UniProtKB.
GO; GO:0031625; F:ubiquitin protein ligase binding; ISO:MGI.
GO; GO:0008270; F:zinc ion binding; ISO:MGI.
GO; GO:0014898; P:cardiac muscle hypertrophy in response to stress; IMP:MGI.
GO; GO:0016577; P:histone demethylation; ISO:MGI.
GO; GO:0070544; P:histone H3-K36 demethylation; ISO:MGI.
GO; GO:0033169; P:histone H3-K9 demethylation; ISO:MGI.
GO; GO:0048712; P:negative regulation of astrocyte differentiation; IEA:Ensembl.
GO; GO:0010507; P:negative regulation of autophagy; ISO:MGI.
GO; GO:0060548; P:negative regulation of cell death; IEA:Ensembl.
GO; GO:0010629; P:negative regulation of gene expression; ISO:MGI.
GO; GO:1900113; P:negative regulation of histone H3-K9 trimethylation; IDA:MGI.
GO; GO:0045892; P:negative regulation of transcription, DNA-templated; ISO:MGI.
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.
Gene3D; 3.30.40.10; -; 2.
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;
Acetylation; Alternative splicing; Chromatin regulator;
Complete proteome; Dioxygenase; Direct protein sequencing; Iron;
Metal-binding; Nucleus; Oxidoreductase; Phosphoprotein;
Reference proteome; Repeat; Transcription; Transcription regulation;
Ubl conjugation; Zinc; Zinc-finger.
INIT_MET 1 1 Removed. {ECO:0000250|UniProtKB:O75164}.
CHAIN 2 1064 Lysine-specific demethylase 4A.
/FTId=PRO_0000183173.
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:0000250}.
METAL 188 188 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 190 190 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 234 234 Zinc. {ECO:0000250|UniProtKB:O75164}.
METAL 240 240 Zinc; via tele nitrogen.
{ECO:0000250|UniProtKB:O75164}.
METAL 276 276 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 306 306 Zinc. {ECO:0000250|UniProtKB:O75164}.
METAL 308 308 Zinc. {ECO:0000250|UniProtKB:O75164}.
BINDING 132 132 2-oxoglutarate.
{ECO:0000250|UniProtKB:O75164}.
BINDING 198 198 2-oxoglutarate.
{ECO:0000250|UniProtKB:O75164}.
BINDING 206 206 2-oxoglutarate.
{ECO:0000250|UniProtKB:O75164}.
BINDING 241 241 2-oxoglutarate.
{ECO:0000250|UniProtKB:B2RXH2}.
BINDING 945 945 Histone H3K4me3. {ECO:0000250}.
BINDING 967 967 Histone H3K4me3. {ECO:0000250}.
BINDING 973 973 Histone H3K4me3. {ECO:0000250}.
MOD_RES 2 2 N-acetylalanine.
{ECO:0000250|UniProtKB:O75164}.
MOD_RES 523 523 Phosphoserine.
{ECO:0000250|UniProtKB:O75164}.
VAR_SEQ 948 1033 SQDCLQLGPPAEGEVVQVRWTDGQVYGAKFVASHPIQMYQV
EFEDGSQLVVKRDDVYTLDEELPKRVKSRLSVASDMRFNEI
FTEK -> MSESGFWQHFGSSGTSSCYCRLDDCGLFACPWS
VSKQKEPLFPGSLSRKSGHAGALSFPEEFRGVSVPCSPLKY
AYISDQIISNSI (in isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_016144.
VAR_SEQ 1034 1064 Missing (in isoform 2).
{ECO:0000303|PubMed:15489334}.
/FTId=VSP_016145.
CONFLICT 339 339 M -> T (in Ref. 1; BAC97997, 2; BAE26217
and 4; AAH28866). {ECO:0000305}.
CONFLICT 1007 1007 D -> G (in Ref. 2; BAE26776).
{ECO:0000305}.
SEQUENCE 1064 AA; 120334 MW; 92FB3E363FDF9E7D CRC64;
MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP KEWKPRTSYD
DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI ANSDKYCTPR YSEFEELERK
YWKNLTFNPP IYGADVNGTL YEQHVDEWNI GRLKTILDLV EKESGITIEG VNTPYLYFGM
WKTSFAWHTE DMDLYSINYL HFGEPKSWYS VPPEHGKRLE RLAKGFFPGS AQSCEAFLRH
KMTLISPLML KKYGIPFDKV TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATRRWIEYG
KQAVLCSCRK DMVKISMDVF VRRFQPERYK LWKAGKDSMV IDHTLPTPEA AEFLKDSGGL
TPRAGSEECP EEDVEAADQG EEGDVKRSLA KHRIGTKRHR VCLEIPQEVS QSELFPKEEL
SSGQYEMTEC PATLAPVRPT HSSVRQVEDS LPFPDYSDPT EVKFEELKNV KLEEEDEEDE
PEAAALDLSV NPASVGGRLV FSGSKKKSSS SLGSTSSQDS VSSDSETAES VSCQGQEKTG
VLTVHSYARG DGKAATGEPS VKKKRSAPRS ISEQELAEVA DEYMLSLEEN KKTKGRRQPL
SKLPRHHPLV LQECGSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN FEAEKEFNEI
MAQQAPHCAV CMIFQTYHQV EFGAFSQSCG DASEPAAQTQ RTKPLIPEMC FTTTGCSTDI
NLSTPYLEED GTSMLVSCKK CSVRVHASCY GVPPAKASEE WMCSRCSANA LEEDCCLCSL
RGGALQRAND DRWVHVSCAV AILEARFVNI AERSPVDVSK IPLPRFKLKC VFCKKRRKRN
AGCCVQCSHG RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALLSIT
AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD CLQLGPPAEG
EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR DDVYTLDEEL PKRVKSRLSV
ASDMRFNEIF TEKEVKQEKK RQRVINSRYR EDYIEPALYR AIME


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E1916r ELISA Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6,Histone arginine demethylase JMJD6,JmjC domain-containing protein 6,Jmjd6,Jumonji domain-containing protein 6,Lysyl-hydroxylase JMJD 96T
U1916r CLIA kit Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6,Histone arginine demethylase JMJD6,JmjC domain-containing protein 6,Jmjd6,Jumonji domain-containing protein 6,Lysyl-hydroxylase 96T
E1916r ELISA kit Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6,Histone arginine demethylase JMJD6,JmjC domain-containing protein 6,Jmjd6,Jumonji domain-containing protein 6,Lysyl-hydroxylase 96T
U1916r CLIA Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6,Histone arginine demethylase JMJD6,JmjC domain-containing protein 6,Jmjd6,Jumonji domain-containing protein 6,Lysyl-hydroxylase JMJD6 96T


 

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