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Q8BW72 (KDM4A_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 105. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1064 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence 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 By similarity.

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

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

Subcellular location

Nucleus By similarity.

Tissue specificity

Widely expressed. Ref.6

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.

Post-translational modification

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.

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.

Sequence caution

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

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q8BW72-1)

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: Q8BW72-2)

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.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed By similarity
Chain2 – 10641063Lysine-specific demethylase 4A
PRO_0000183173

Regions

Domain14 – 5643JmjN
Domain142 – 308167JmjC
Domain897 – 95458Tudor 1
Domain955 – 101157Tudor 2
Zinc finger709 – 76759PHD-type 1
Zinc finger829 – 88557PHD-type 2
Region597 – 63842Interaction with NCOR1 By similarity

Sites

Metal binding1881Iron; catalytic By similarity
Metal binding1901Iron; catalytic By similarity
Metal binding2341Zinc By similarity
Metal binding2401Zinc By similarity
Metal binding2761Iron; catalytic By similarity
Metal binding3061Zinc By similarity
Metal binding3081Zinc By similarity
Binding site1321Alpha-ketoglutarate By similarity
Binding site1981Alpha-ketoglutarate By similarity
Binding site2061Alpha-ketoglutarate By similarity
Binding site9451Histone H3K4me3 By similarity
Binding site9671Histone H3K4me3 By similarity
Binding site9731Histone H3K4me3 By similarity

Amino acid modifications

Modified residue21N-acetylalanine By similarity

Natural variations

Alternative sequence948 – 103386SQDCL…IFTEK → MSESGFWQHFGSSGTSSCYC RLDDCGLFACPWSVSKQKEP LFPGSLSRKSGHAGALSFPE EFRGVSVPCSPLKYAYISDQ IISNSI in isoform 2.
VSP_016144
Alternative sequence1034 – 106431Missing in isoform 2.
VSP_016145

Experimental info

Sequence conflict3391M → T in BAC97997. Ref.1
Sequence conflict3391M → T in BAE26217. Ref.2
Sequence conflict3391M → T in AAH28866. Ref.4
Sequence conflict10071D → G in BAE26776. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 27, 2011. Version 3.
Checksum: 92FB3E363FDF9E7D

FASTA1,064120,334
        10         20         30         40         50         60 
MASESETLNP SARIMTFYPT MEEFRNFSRY IAYIESQGAH RAGLAKVVPP KEWKPRTSYD 

        70         80         90        100        110        120 
DIDDLVIPAP IQQLVTGQSG LFTQYNIQKK AMTVREFRKI ANSDKYCTPR YSEFEELERK 

       130        140        150        160        170        180 
YWKNLTFNPP IYGADVNGTL YEQHVDEWNI GRLKTILDLV 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 VRRFQPERYK LWKAGKDSMV IDHTLPTPEA AEFLKDSGGL 

       370        380        390        400        410        420 
TPRAGSEECP EEDVEAADQG EEGDVKRSLA KHRIGTKRHR VCLEIPQEVS QSELFPKEEL 

       430        440        450        460        470        480 
SSGQYEMTEC PATLAPVRPT HSSVRQVEDS LPFPDYSDPT EVKFEELKNV KLEEEDEEDE 

       490        500        510        520        530        540 
PEAAALDLSV NPASVGGRLV FSGSKKKSSS SLGSTSSQDS VSSDSETAES VSCQGQEKTG 

       550        560        570        580        590        600 
VLTVHSYARG DGKAATGEPS VKKKRSAPRS ISEQELAEVA DEYMLSLEEN KKTKGRRQPL 

       610        620        630        640        650        660 
SKLPRHHPLV LQECGSDDET SEQLTPEEEA EETEAWAKPL SQLWQNRPPN FEAEKEFNEI 

       670        680        690        700        710        720 
MAQQAPHCAV CMIFQTYHQV EFGAFSQSCG DASEPAAQTQ RTKPLIPEMC FTTTGCSTDI 

       730        740        750        760        770        780 
NLSTPYLEED GTSMLVSCKK CSVRVHASCY GVPPAKASEE WMCSRCSANA LEEDCCLCSL 

       790        800        810        820        830        840 
RGGALQRAND DRWVHVSCAV AILEARFVNI AERSPVDVSK IPLPRFKLKC VFCKKRRKRN 

       850        860        870        880        890        900 
AGCCVQCSHG RCPTAFHVSC AQAAGVMMQP DDWPFVVFIT CFRHKIPNLE RAKGALLSIT 

       910        920        930        940        950        960 
AGQKVISKHK NGRFYQCEVV RLTTETFYEV NFDDGSFSDN LYPEDIVSQD CLQLGPPAEG 

       970        980        990       1000       1010       1020 
EVVQVRWTDG QVYGAKFVAS HPIQMYQVEF EDGSQLVVKR DDVYTLDEEL PKRVKSRLSV 

      1030       1040       1050       1060 
ASDMRFNEIF TEKEVKQEKK RQRVINSRYR EDYIEPALYR AIME 

« Hide

Isoform 2 [UniParc].

Checksum: A0485D01A1AEDF4D
Show »

FASTA1,033115,963

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Lineage-specific biology revealed by a finished genome assembly of the mouse."
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. expand/collapse author list , 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.
PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS51282.1. [Q8BW72-1]
RefSeqNP_001155295.1. NM_001161823.1. [Q8BW72-1]
NP_759014.2. NM_172382.2.
XP_006503073.1. XM_006503010.1. [Q8BW72-1]
UniGeneMm.234234.

3D structure databases

ProteinModelPortalQ8BW72.
SMRQ8BW72. Positions 3-355, 733-770, 821-869, 898-1011.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid230999. 4 interactions.

PTM databases

PhosphoSiteQ8BW72.

Proteomic databases

PaxDbQ8BW72.
PRIDEQ8BW72.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000097911; ENSMUSP00000095524; ENSMUSG00000033326. [Q8BW72-1]
ENSMUST00000106403; ENSMUSP00000102011; ENSMUSG00000033326. [Q8BW72-1]
ENSMUST00000106406; ENSMUSP00000102014; ENSMUSG00000033326. [Q8BW72-1]
GeneID230674.
KEGGmmu:230674.
UCSCuc008ujn.2. mouse. [Q8BW72-1]

Organism-specific databases

CTD9682.
MGIMGI:2446210. Kdm4a.
RougeSearch...

Phylogenomic databases

eggNOGCOG5141.
GeneTreeENSGT00530000063342.
HOVERGENHBG080483.
InParanoidA2A8L8.
KOK06709.
OMARKRTAGC.
OrthoDBEOG7TQV03.
TreeFamTF106449.

Gene expression databases

BgeeQ8BW72.
CleanExMM_JMJD2A.
GenevestigatorQ8BW72.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR003347. JmjC_dom.
IPR003349. TF_JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSKdm4A. mouse.
NextBio380043.
PROQ8BW72.
SOURCESearch...

Entry information

Entry nameKDM4A_MOUSE
AccessionPrimary (citable) accession number: Q8BW72
Secondary accession number(s): A2A8L8 expand/collapse secondary AC list , Q3UKM5, Q3UM81, Q3UWV2, Q6ZQ72, Q8K137
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot