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Q3UXZ9 (KDM5A_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 82. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 5A

EC=1.14.11.-
Alternative name(s):
Histone demethylase JARID1A
Jumonji/ARID domain-containing protein 1A
Retinoblastoma-binding protein 2
Short name=RBBP-2
Gene names
Name:Kdm5a
Synonyms:Jarid1a, Rbp2
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1690 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation. May participate in transcriptional repression of cytokines such as CXCL12. Ref.5 Ref.6

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

Interacts with RB1, ESR1, MYC, MYCN and LMO2 By similarity. Interacts with SUZ12; the interaction is direct. Ref.7

Subcellular location

Nucleusnucleolus By similarity. Nucleus. Note: Occupies promoters of genes involved in RNA metabolism and mitochondrial function. Ref.7

Domain

The GSGFP motif is required for the interaction with SUZ12. Ref.7

Disruption phenotype

Mice are grossly normal, except that they exhibit behavioral abnormalities when held upside down by the tail, and slight hematological defects. Ref.5

Sequence similarities

Belongs to the JARID1 histone demethylase family.

Contains 1 ARID domain.

Contains 1 JmjC domain.

Contains 1 JmjN domain.

Contains 3 PHD-type zinc fingers.

Sequence caution

The sequence BAE22414.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   DomainRepeat
Zinc-finger
   LigandIron
Metal-binding
Zinc
   Molecular functionChromatin regulator
Developmental protein
Dioxygenase
Oxidoreductase
   PTMPhosphoprotein
   Technical termComplete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processchromatin modification

Inferred from electronic annotation. Source: UniProtKB-KW

multicellular organismal development

Inferred from electronic annotation. Source: UniProtKB-KW

positive regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcyclin-dependent protein kinase activating kinase holoenzyme complex

Inferred from electronic annotation. Source: Ensembl

cytoplasm

Inferred from electronic annotation. Source: Ensembl

nucleolus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

chromatin binding

Inferred from direct assay Ref.7. Source: UniProtKB

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors

Inferred from electronic annotation. Source: InterPro

protein binding

Inferred from physical interaction Ref.7. Source: UniProtKB

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Suz12Q80U702EBI-2531441,EBI-2526494

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 16901690Lysine-specific demethylase 5A
PRO_0000292411

Regions

Domain19 – 6042JmjN
Domain84 – 17491ARID
Domain437 – 603167JmjC
Zinc finger293 – 34351PHD-type 1
Zinc finger1153 – 121058PHD-type 2
Zinc finger1599 – 165355PHD-type 3
Region1622 – 169069Interaction with LMO2 By similarity
Motif419 – 4235GSGFP motif
Compositional bias1484 – 157996Lys-rich

Sites

Metal binding4831Iron; catalytic By similarity
Metal binding4861Iron; catalytic By similarity
Metal binding5711Iron; catalytic By similarity

Amino acid modifications

Modified residue11111Phosphoserine Ref.8
Modified residue13311Phosphoserine By similarity
Modified residue15981Phosphoserine By similarity
Modified residue16031Phosphoserine By similarity
Modified residue16661Phosphoserine By similarity

Experimental info

Sequence conflict101A → S in BAE38548. Ref.2
Sequence conflict141V → R in BAE38548. Ref.2
Sequence conflict171P → A in BAE38548. Ref.2
Sequence conflict241P → A in BAE38548. Ref.2
Sequence conflict5441V → A in BAE38548. Ref.2
Sequence conflict12721A → P in BAE22414. Ref.2

Sequences

Sequence LengthMass (Da)Tools
Q3UXZ9 [UniParc].

Last modified June 26, 2007. Version 2.
Checksum: EFCF56AAAA51F0FC

FASTA1,690192,216
        10         20         30         40         50         60 
MASVGPGGYA AEFVPPPECP VFEPSWEEFT DPLSFIGRIR PFAEKTGICK IRPPKDWQPP 

        70         80         90        100        110        120 
FACEVKTFRF TPRVQRLNEL EAMTRVRLDF LDQLAKFWEL QGSTLKIPVV ERKILDLYAL 

       130        140        150        160        170        180 
SKIVASKGGF EIVTKEKKWS KVGSRLGYLP GKGTGSLLKS HYERILYPYE LFQSGVSLMG 

       190        200        210        220        230        240 
VQMPDLDLKE KVEAEVLSTD IQPSPERGTR MNIPPKRTRR VKSQSDSGEV NRNTELKKLQ 

       250        260        270        280        290        300 
IFGAGPKVVG LAVGAKDKED EVTRRRKVTN RSDAFNMQMR QRKGTLSVNF VDLYVCMFCG 

       310        320        330        340        350        360 
RGNNEDKLLL CDGCDDSYHT FCLLPPLPDV PKGDWRCPKC VAEECNKPRE AFGFEQAVRE 

       370        380        390        400        410        420 
YTLQSFGEMA DNFKSDYFNM PVHMVPTELV EKEFWRLVSS IEEDVIVEYG ADISSKDFGS 

       430        440        450        460        470        480 
GFPKKDGQRK MLPEEEEYAL SGWNLNNMPV LEQSVLAHIN VDISGMKVPW LYVGMCFSSF 

       490        500        510        520        530        540 
CWHIEDHWSY SINYLHWGEP KTWYGVPSHA AEQLEEVMRE LAPELFESQP DLLHQLVTIM 

       550        560        570        580        590        600 
NPNVLMEHGV PVYRTNQCAG EFVVTFPRAY HSGFNQGYNF AEAVNFCTAD WLPIGRQCVN 

       610        620        630        640        650        660 
HYRRLRRHCV FSHEELIFKM AADPECLDVG LAAMVCKELT LMTEEETRLR ESVVQMGVVM 

       670        680        690        700        710        720 
SEEEVFELVP DDERQCSACR TTCFLSALTC SCNPERLVCL YHPTDLCSCP MQNKCLRYRY 

       730        740        750        760        770        780 
PLEDLPSLLY GVKVRAQSYD TWVNRVTEAL SASFNHKKDL IELRVMLEDA EDRKYPENDL 

       790        800        810        820        830        840 
FRKLRDAVKE AETCGSVAQL LLSKKQKHRQ SSDSGKTRTK LTVEELKAFV QQLVSLPCVI 

       850        860        870        880        890        900 
SQTRQVKNLL DDVEEFHERA QEAMMDETPD SSKLQMLIDM GSSLYVELPE LPRLKQELQQ 

       910        920        930        940        950        960 
ARWLDEVRLT LSDPQQVTLD VMKKLIDSGV GLAPHHAVEK AMAELQELLT VSERWEEKAK 

       970        980        990       1000       1010       1020 
VCLQARPRHS MANLENIVNE AKNIPAFLPN VLSLKEALQK AREWTAKVEA IQSGNNYAYL 

      1030       1040       1050       1060       1070       1080 
EQLESLSAKG RPIPVRLDAL PQVESQVAAA RAWRERTGRT FLKKNSSHTL LQVLSPRTDI 

      1090       1100       1110       1120       1130       1140 
GVYGSGKNRR KKVKEIIEKE KEKDLDLEPL SDLEEGLEES RDTAMVVAVF KEREQKEIEA 

      1150       1160       1170       1180       1190       1200 
MHSLRAANLA KMTIVERIEE VKFCICRKTA SGFMLQCELC KDWFHNSCVP LPKSSSQKKG 

      1210       1220       1230       1240       1250       1260 
SSWQAKDVKF LCPLCMRSRR PRLETILSLL VSLQKLPVRL PEGEALQCLT ERAMSWQDKA 

      1270       1280       1290       1300       1310       1320 
RQALATDELS SALAKLSVLS QRMVEQAARE KTEKIISAEL QKAAANPDLQ GHLPSFQQSA 

      1330       1340       1350       1360       1370       1380 
FNRVVSSVSS SPHQTMDYDD EETDSDEDIR ETYGYDMKDT ASVKSSSSLE PNLFCDEEIP 

      1390       1400       1410       1420       1430       1440 
IKSEEVVTHM WTAPSFCAEH AYSSASKSCS QGSSTPRKQP RKSPLVPRSL EPPVLELSPG 

      1450       1460       1470       1480       1490       1500 
AKAQLEELMM VGDLLEVSLD ETQHIWRILQ ATHPPSEDRF LHIMEDDSIE EKPLKMKGKD 

      1510       1520       1530       1540       1550       1560 
SSEKKRKRKL EKVEQLFGEG KQKTKELKKI DKPKKKKLKL NVDKSKELNK LAKKLAKEEE 

      1570       1580       1590       1600       1610       1620 
RKKKKEKAAA AKVELVKEST EKKRERKVLD IPSKYDWSGA EESDDENAVC AAQNCQRPCK 

      1630       1640       1650       1660       1670       1680 
DKVDWVQCDG GCDEWFHQVC VGVSAEMAEN EDYICINCAK KQGPDSPGQA PPPPFLMSYK 

      1690 
LPMEDLKETS 

« Hide

References

« Hide 'large scale' references
[1]"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.
[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] OF 1-1552.
Strain: C57BL/6J.
Tissue: Lung and Olfactory bulb.
[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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-1099.
Strain: C57BL/6J.
Tissue: Germ cell.
[4]Lubec G., Sunyer B., Chen W.-Q.
Submitted (JAN-2009) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 1538-1546, IDENTIFICATION BY MASS SPECTROMETRY.
Strain: OF1.
Tissue: Hippocampus.
[5]"The retinoblastoma binding protein RBP2 is an H3K4 demethylase."
Klose R.J., Yan Q., Tothova Z., Yamane K., Erdjument-Bromage H., Tempst P., Gilliland D.G., Zhang Y., Kaelin W.G. Jr.
Cell 128:889-900(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, DISRUPTION PHENOTYPE.
[6]"RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3."
Christensen J., Agger K., Cloos P.A.C., Pasini D., Rose S., Sennels L., Rappsilber J., Hansen K.H., Salcini A.E., Helin K.
Cell 128:1063-1076(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells."
Peng J.C., Valouev A., Swigut T., Zhang J., Zhao Y., Sidow A., Wysocka J.
Cell 139:1290-1302(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, DOMAIN GSGFP MOTIF, INTERACTION WITH SUZ12.
[8]"The phagosomal proteome in interferon-gamma-activated macrophages."
Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1111, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AC155720 Genomic DNA. No translation available.
AC078896 Genomic DNA. No translation available.
AK135085 mRNA. Translation: BAE22414.1. Different initiation.
AK144877 mRNA. Translation: BAE26113.1.
AK166055 mRNA. Translation: BAE38548.1.
BC080691 mRNA. Translation: AAH80691.1. Different termination.
CCDSCCDS51889.1.
RefSeqNP_666109.2. NM_145997.2.
UniGeneMm.404761.
Mm.463658.

3D structure databases

ProteinModelPortalQ3UXZ9.
SMRQ3UXZ9. Positions 18-81, 84-175, 260-585, 1162-1221, 1608-1659.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid229572. 1 interaction.
IntActQ3UXZ9. 1 interaction.

PTM databases

PhosphoSiteQ3UXZ9.

Proteomic databases

PaxDbQ3UXZ9.
PRIDEQ3UXZ9.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000100996; ENSMUSP00000098558; ENSMUSG00000030180.
GeneID214899.
KEGGmmu:214899.
UCSCuc009dne.2. mouse.

Organism-specific databases

CTD5927.
MGIMGI:2136980. Kdm5a.

Phylogenomic databases

eggNOGNOG327026.
GeneTreeENSGT00530000063118.
HOGENOMHOG000290719.
InParanoidQ3UXZ9.
KOK11446.
OMACVAHYRR.
PhylomeDBQ3UXZ9.
TreeFamTF106476.

Gene expression databases

ArrayExpressQ3UXZ9.
BgeeQ3UXZ9.
CleanExMM_RBP2.
GenevestigatorQ3UXZ9.

Family and domain databases

Gene3D1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProIPR001606. ARID/BRIGHT_DNA-bd.
IPR003347. JmjC_dom.
IPR013637. Lys_sp_deMease_like_dom.
IPR003349. TF_JmjN.
IPR019786. Zinc_finger_PHD-type_CS.
IPR004198. Znf_C5HC2.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamPF01388. ARID. 1 hit.
PF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
PF00628. PHD. 2 hits.
PF08429. PLU-1. 1 hit.
PF02928. zf-C5HC2. 1 hit.
[Graphical view]
SMARTSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
[Graphical view]
SUPFAMSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEPS51011. ARID. 1 hit.
PS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
PS01359. ZF_PHD_1. 2 hits.
PS50016. ZF_PHD_2. 3 hits.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSKDM5A. mouse.
NextBio374501.
PROQ3UXZ9.
SOURCESearch...

Entry information

Entry nameKDM5A_MOUSE
AccessionPrimary (citable) accession number: Q3UXZ9
Secondary accession number(s): Q3TM94, Q3UMI5, Q66JZ3
Entry history
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: June 26, 2007
Last modified: July 9, 2014
This is version 82 of the entry and version 2 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