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Q8BW72

- KDM4A_MOUSE

UniProt

Q8BW72 - KDM4A_MOUSE

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Protein
Lysine-specific demethylase 4A
Gene
Kdm4a, Jhdm3a, Jmjd2, Jmjd2a, Kiaa0677
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.

Cofactori

Binds 1 Fe2+ ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei132 – 1321Alpha-ketoglutarate By similarity
Metal bindingi188 – 1881Iron; catalytic By similarity
Metal bindingi190 – 1901Iron; catalytic By similarity
Binding sitei198 – 1981Alpha-ketoglutarate By similarity
Binding sitei206 – 2061Alpha-ketoglutarate By similarity
Metal bindingi234 – 2341Zinc By similarity
Metal bindingi240 – 2401Zinc By similarity
Metal bindingi276 – 2761Iron; catalytic By similarity
Metal bindingi306 – 3061Zinc By similarity
Metal bindingi308 – 3081Zinc By similarity
Binding sitei945 – 9451Histone H3K4me3 By similarity
Binding sitei967 – 9671Histone H3K4me3 By similarity
Binding sitei973 – 9731Histone H3K4me3 By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri709 – 76759PHD-type 1
Add
BLAST
Zinc fingeri829 – 88557PHD-type 2
Add
BLAST

GO - Molecular functioni

  1. histone demethylase activity (H3-K36 specific) Source: Ensembl
  2. methylated histone binding Source: UniProtKB
  3. zinc ion binding Source: InterPro

GO - Biological processi

  1. cardiac muscle hypertrophy in response to stress Source: MGI
  2. negative regulation of transcription, DNA-templated Source: Ensembl
  3. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
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 namesi
Name:Kdm4a
Synonyms:Jhdm3a, Jmjd2, Jmjd2a, Kiaa0677
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 4

Organism-specific databases

MGIiMGI:2446210. Kdm4a.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. centrosome Source: Ensembl
  2. cytoplasm Source: Ensembl
  3. nucleolus Source: Ensembl
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed By similarity
Chaini2 – 10641063Lysine-specific demethylase 4A
PRO_0000183173Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanine By similarity

Post-translational modificationi

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.

Keywords - PTMi

Acetylation, Ubl conjugation

Proteomic databases

PaxDbiQ8BW72.
PRIDEiQ8BW72.

PTM databases

PhosphoSiteiQ8BW72.

Expressioni

Tissue specificityi

Widely expressed.1 Publication

Gene expression databases

BgeeiQ8BW72.
CleanExiMM_JMJD2A.
GenevestigatoriQ8BW72.

Interactioni

Subunit structurei

Interacts with histone deacetylase proteins HDAC1, HDAC2 and HDAC3. Interacts with RB and NCOR1 By similarity.

Protein-protein interaction databases

BioGridi230999. 4 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ8BW72.
SMRiQ8BW72. Positions 3-355, 733-770, 821-869, 898-1011.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 5643JmjN
Add
BLAST
Domaini142 – 308167JmjC
Add
BLAST
Domaini897 – 95458Tudor 1
Add
BLAST
Domaini955 – 101157Tudor 2
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni597 – 63842Interaction with NCOR1 By similarity
Add
BLAST

Domaini

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.

Sequence similaritiesi

Contains 1 JmjC domain.
Contains 1 JmjN domain.
Contains 2 Tudor domains.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiCOG5141.
GeneTreeiENSGT00530000063342.
HOVERGENiHBG080483.
InParanoidiA2A8L8.
KOiK06709.
OMAiRKRTAGC.
OrthoDBiEOG7TQV03.
TreeFamiTF106449.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR003349. TF_JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q8BW72-1) [UniParc]FASTAAdd to Basket

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.

« Hide

MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP     50
KEWKPRTSYD DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI 100
ANSDKYCTPR YSEFEELERK YWKNLTFNPP IYGADVNGTL YEQHVDEWNI 150
GRLKTILDLV EKESGITIEG VNTPYLYFGM WKTSFAWHTE DMDLYSINYL 200
HFGEPKSWYS VPPEHGKRLE RLAKGFFPGS AQSCEAFLRH KMTLISPLML 250
KKYGIPFDKV TQEAGEFMIT FPYGYHAGFN HGFNCAESTN FATRRWIEYG 300
KQAVLCSCRK DMVKISMDVF VRRFQPERYK LWKAGKDSMV IDHTLPTPEA 350
AEFLKDSGGL TPRAGSEECP EEDVEAADQG EEGDVKRSLA KHRIGTKRHR 400
VCLEIPQEVS QSELFPKEEL SSGQYEMTEC PATLAPVRPT HSSVRQVEDS 450
LPFPDYSDPT EVKFEELKNV KLEEEDEEDE PEAAALDLSV NPASVGGRLV 500
FSGSKKKSSS SLGSTSSQDS VSSDSETAES VSCQGQEKTG VLTVHSYARG 550
DGKAATGEPS VKKKRSAPRS ISEQELAEVA DEYMLSLEEN KKTKGRRQPL 600
SKLPRHHPLV LQECGSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN 650
FEAEKEFNEI MAQQAPHCAV CMIFQTYHQV EFGAFSQSCG DASEPAAQTQ 700
RTKPLIPEMC FTTTGCSTDI NLSTPYLEED GTSMLVSCKK CSVRVHASCY 750
GVPPAKASEE WMCSRCSANA LEEDCCLCSL RGGALQRAND DRWVHVSCAV 800
AILEARFVNI AERSPVDVSK IPLPRFKLKC VFCKKRRKRN AGCCVQCSHG 850
RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALLSIT 900
AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD 950
CLQLGPPAEG EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR 1000
DDVYTLDEEL PKRVKSRLSV ASDMRFNEIF TEKEVKQEKK RQRVINSRYR 1050
EDYIEPALYR AIME 1064
Length:1,064
Mass (Da):120,334
Last modified:July 27, 2011 - v3
Checksum:i92FB3E363FDF9E7D
GO
Isoform 2 (identifier: Q8BW72-2) [UniParc]FASTAAdd to Basket

The sequence of this isoform differs from the canonical sequence as follows:
     948-1033: SQDCLQLGPP...MRFNEIFTEK → MSESGFWQHF...ISDQIISNSI
     1034-1064: Missing.

Note: No experimental confirmation available.

Show »
Length:1,033
Mass (Da):115,963
Checksum:iA0485D01A1AEDF4D
GO

Sequence cautioni

The sequence BAC97997.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei948 – 103386SQDCL…IFTEK → MSESGFWQHFGSSGTSSCYC RLDDCGLFACPWSVSKQKEP LFPGSLSRKSGHAGALSFPE EFRGVSVPCSPLKYAYISDQ IISNSI in isoform 2.
VSP_016144Add
BLAST
Alternative sequencei1034 – 106431Missing in isoform 2.
VSP_016145Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti339 – 3391M → T in BAC97997. 1 Publication
Sequence conflicti339 – 3391M → T in BAE26217. 1 Publication
Sequence conflicti339 – 3391M → T in AAH28866. 1 Publication
Sequence conflicti1007 – 10071D → G in BAE26776. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK129187 mRNA. Translation: BAC97997.1. Different initiation.
AK054095 mRNA. Translation: BAC35653.1.
AK136085 mRNA. Translation: BAE22812.1.
AK145066 mRNA. Translation: BAE26217.1.
AK145947 mRNA. Translation: BAE26776.1.
AL626764 Genomic DNA. Translation: CAM27385.1.
BC028866 mRNA. Translation: AAH28866.1.
CCDSiCCDS51282.1. [Q8BW72-1]
RefSeqiNP_001155295.1. NM_001161823.1. [Q8BW72-1]
NP_759014.2. NM_172382.2.
XP_006503073.1. XM_006503010.1. [Q8BW72-1]
UniGeneiMm.234234.

Genome annotation databases

EnsembliENSMUST00000097911; ENSMUSP00000095524; ENSMUSG00000033326. [Q8BW72-1]
ENSMUST00000106403; ENSMUSP00000102011; ENSMUSG00000033326. [Q8BW72-1]
ENSMUST00000106406; ENSMUSP00000102014; ENSMUSG00000033326. [Q8BW72-1]
GeneIDi230674.
KEGGimmu:230674.
UCSCiuc008ujn.2. mouse. [Q8BW72-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AK129187 mRNA. Translation: BAC97997.1 . Different initiation.
AK054095 mRNA. Translation: BAC35653.1 .
AK136085 mRNA. Translation: BAE22812.1 .
AK145066 mRNA. Translation: BAE26217.1 .
AK145947 mRNA. Translation: BAE26776.1 .
AL626764 Genomic DNA. Translation: CAM27385.1 .
BC028866 mRNA. Translation: AAH28866.1 .
CCDSi CCDS51282.1. [Q8BW72-1 ]
RefSeqi NP_001155295.1. NM_001161823.1. [Q8BW72-1 ]
NP_759014.2. NM_172382.2.
XP_006503073.1. XM_006503010.1. [Q8BW72-1 ]
UniGenei Mm.234234.

3D structure databases

ProteinModelPortali Q8BW72.
SMRi Q8BW72. Positions 3-355, 733-770, 821-869, 898-1011.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 230999. 4 interactions.

PTM databases

PhosphoSitei Q8BW72.

Proteomic databases

PaxDbi Q8BW72.
PRIDEi Q8BW72.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000097911 ; ENSMUSP00000095524 ; ENSMUSG00000033326 . [Q8BW72-1 ]
ENSMUST00000106403 ; ENSMUSP00000102011 ; ENSMUSG00000033326 . [Q8BW72-1 ]
ENSMUST00000106406 ; ENSMUSP00000102014 ; ENSMUSG00000033326 . [Q8BW72-1 ]
GeneIDi 230674.
KEGGi mmu:230674.
UCSCi uc008ujn.2. mouse. [Q8BW72-1 ]

Organism-specific databases

CTDi 9682.
MGIi MGI:2446210. Kdm4a.
Rougei Search...

Phylogenomic databases

eggNOGi COG5141.
GeneTreei ENSGT00530000063342.
HOVERGENi HBG080483.
InParanoidi A2A8L8.
KOi K06709.
OMAi RKRTAGC.
OrthoDBi EOG7TQV03.
TreeFami TF106449.

Miscellaneous databases

ChiTaRSi Kdm4A. mouse.
NextBioi 380043.
PROi Q8BW72.
SOURCEi Search...

Gene expression databases

Bgeei Q8BW72.
CleanExi MM_JMJD2A.
Genevestigatori Q8BW72.

Family and domain databases

Gene3Di 3.30.40.10. 1 hit.
InterProi IPR003347. JmjC_dom.
IPR003349. TF_JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view ]
Pfami PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view ]
SMARTi SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view ]
SUPFAMi SSF57903. SSF57903. 1 hit.
PROSITEi PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "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."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H.
    DNA Res. 10:167-180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Tissue: Embryonic tail.
  2. "The transcriptional landscape of the mammalian genome."
    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.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: C57BL/6J.
    Tissue: Embryo, Mammary gland, Oviduct and Placenta.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  4. "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] (ISOFORM 2).
    Strain: FVB/N.
    Tissue: Colon.
  5. Lubec G., Sunyer B., Chen W.-Q.
    Submitted (JAN-2009) to UniProtKB
    Cited for: PROTEIN SEQUENCE OF 499-505, IDENTIFICATION BY MASS SPECTROMETRY.
    Strain: OF1.
    Tissue: Hippocampus.
  6. "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] [Europe PMC] [Abstract]
    Cited for: TISSUE SPECIFICITY.

Entry informationi

Entry nameiKDM4A_MOUSE
AccessioniPrimary (citable) accession number: Q8BW72
Secondary accession number(s): A2A8L8
, Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, Q8K137
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: July 27, 2011
Last modified: July 9, 2014
This is version 105 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi