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Q3UXZ9

- KDM5A_MOUSE

UniProt

Q3UXZ9 - KDM5A_MOUSE

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Protein
Lysine-specific demethylase 5A
Gene
Kdm5a, Jarid1a, Rbp2
Organism
Mus musculus (Mouse)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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 CXCL12.2 Publications

Cofactori

Binds 1 Fe2+ ion per subunit By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi483 – 4831Iron; catalytic By similarity
Metal bindingi486 – 4861Iron; catalytic By similarity
Metal bindingi571 – 5711Iron; catalytic By similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri293 – 34351PHD-type 1
Add
BLAST
Zinc fingeri1153 – 121058PHD-type 2
Add
BLAST
Zinc fingeri1599 – 165355PHD-type 3
Add
BLAST

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. chromatin binding Source: UniProtKB
  3. 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 Source: InterPro
  4. protein binding Source: UniProtKB
  5. zinc ion binding Source: InterPro
Complete GO annotation...

GO - Biological processi

  1. chromatin modification Source: UniProtKB-KW
  2. multicellular organismal development Source: UniProtKB-KW
  3. positive regulation of transcription, DNA-templated Source: Ensembl
  4. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:Kdm5a
Synonyms:Jarid1a, Rbp2
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 6

Organism-specific databases

MGIiMGI:2136980. Kdm5a.

Subcellular locationi

Nucleusnucleolus By similarity. Nucleus
Note: Occupies promoters of genes involved in RNA metabolism and mitochondrial function.1 Publication

GO - Cellular componenti

  1. cyclin-dependent protein kinase activating kinase holoenzyme complex Source: Ensembl
  2. cytoplasm Source: Ensembl
  3. nucleolus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Disruption phenotypei

Mice are grossly normal, except that they exhibit behavioral abnormalities when held upside down by the tail, and slight hematological defects.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 16901690Lysine-specific demethylase 5A
PRO_0000292411Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1111 – 11111Phosphoserine1 Publication
Modified residuei1331 – 13311Phosphoserine By similarity
Modified residuei1598 – 15981Phosphoserine By similarity
Modified residuei1603 – 16031Phosphoserine By similarity
Modified residuei1666 – 16661Phosphoserine By similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ3UXZ9.
PRIDEiQ3UXZ9.

PTM databases

PhosphoSiteiQ3UXZ9.

Expressioni

Gene expression databases

ArrayExpressiQ3UXZ9.
BgeeiQ3UXZ9.
CleanExiMM_RBP2.
GenevestigatoriQ3UXZ9.

Interactioni

Subunit structurei

Interacts with RB1, ESR1, MYC, MYCN and LMO2 By similarity. Interacts with SUZ12; the interaction is direct.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
Suz12Q80U702EBI-2531441,EBI-2526494

Protein-protein interaction databases

BioGridi229572. 1 interaction.
IntActiQ3UXZ9. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ3UXZ9.
SMRiQ3UXZ9. Positions 18-81, 84-175, 260-585, 1162-1221, 1608-1659.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini19 – 6042JmjN
Add
BLAST
Domaini84 – 17491ARID
Add
BLAST
Domaini437 – 603167JmjC
Add
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni1622 – 169069Interaction with LMO2 By similarity
Add
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi419 – 4235GSGFP motif

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi1484 – 157996Lys-rich
Add
BLAST

Domaini

The GSGFP motif is required for the interaction with SUZ12.1 Publication

Sequence similaritiesi

Contains 1 ARID domain.
Contains 1 JmjC domain.
Contains 1 JmjN domain.

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG327026.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ3UXZ9.
KOiK11446.
OMAiCVAHYRR.
PhylomeDBiQ3UXZ9.
TreeFamiTF106476.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProiIPR001606. 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]
PfamiPF01388. 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]
SMARTiSM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
[Graphical view]
SUPFAMiSSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEiPS51011. 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]

Sequencei

Sequence statusi: Complete.

Q3UXZ9-1 [UniParc]FASTAAdd to Basket

« Hide

MASVGPGGYA AEFVPPPECP VFEPSWEEFT DPLSFIGRIR PFAEKTGICK     50
IRPPKDWQPP FACEVKTFRF TPRVQRLNEL EAMTRVRLDF LDQLAKFWEL 100
QGSTLKIPVV ERKILDLYAL SKIVASKGGF EIVTKEKKWS KVGSRLGYLP 150
GKGTGSLLKS HYERILYPYE LFQSGVSLMG VQMPDLDLKE KVEAEVLSTD 200
IQPSPERGTR MNIPPKRTRR VKSQSDSGEV NRNTELKKLQ IFGAGPKVVG 250
LAVGAKDKED EVTRRRKVTN RSDAFNMQMR QRKGTLSVNF VDLYVCMFCG 300
RGNNEDKLLL CDGCDDSYHT FCLLPPLPDV PKGDWRCPKC VAEECNKPRE 350
AFGFEQAVRE YTLQSFGEMA DNFKSDYFNM PVHMVPTELV EKEFWRLVSS 400
IEEDVIVEYG ADISSKDFGS GFPKKDGQRK MLPEEEEYAL SGWNLNNMPV 450
LEQSVLAHIN VDISGMKVPW LYVGMCFSSF CWHIEDHWSY SINYLHWGEP 500
KTWYGVPSHA AEQLEEVMRE LAPELFESQP DLLHQLVTIM NPNVLMEHGV 550
PVYRTNQCAG EFVVTFPRAY HSGFNQGYNF AEAVNFCTAD WLPIGRQCVN 600
HYRRLRRHCV FSHEELIFKM AADPECLDVG LAAMVCKELT LMTEEETRLR 650
ESVVQMGVVM SEEEVFELVP DDERQCSACR TTCFLSALTC SCNPERLVCL 700
YHPTDLCSCP MQNKCLRYRY PLEDLPSLLY GVKVRAQSYD TWVNRVTEAL 750
SASFNHKKDL IELRVMLEDA EDRKYPENDL FRKLRDAVKE AETCGSVAQL 800
LLSKKQKHRQ SSDSGKTRTK LTVEELKAFV QQLVSLPCVI SQTRQVKNLL 850
DDVEEFHERA QEAMMDETPD SSKLQMLIDM GSSLYVELPE LPRLKQELQQ 900
ARWLDEVRLT LSDPQQVTLD VMKKLIDSGV GLAPHHAVEK AMAELQELLT 950
VSERWEEKAK VCLQARPRHS MANLENIVNE AKNIPAFLPN VLSLKEALQK 1000
AREWTAKVEA IQSGNNYAYL EQLESLSAKG RPIPVRLDAL PQVESQVAAA 1050
RAWRERTGRT FLKKNSSHTL LQVLSPRTDI GVYGSGKNRR KKVKEIIEKE 1100
KEKDLDLEPL SDLEEGLEES RDTAMVVAVF KEREQKEIEA MHSLRAANLA 1150
KMTIVERIEE VKFCICRKTA SGFMLQCELC KDWFHNSCVP LPKSSSQKKG 1200
SSWQAKDVKF LCPLCMRSRR PRLETILSLL VSLQKLPVRL PEGEALQCLT 1250
ERAMSWQDKA RQALATDELS SALAKLSVLS QRMVEQAARE KTEKIISAEL 1300
QKAAANPDLQ GHLPSFQQSA FNRVVSSVSS SPHQTMDYDD EETDSDEDIR 1350
ETYGYDMKDT ASVKSSSSLE PNLFCDEEIP IKSEEVVTHM WTAPSFCAEH 1400
AYSSASKSCS QGSSTPRKQP RKSPLVPRSL EPPVLELSPG AKAQLEELMM 1450
VGDLLEVSLD ETQHIWRILQ ATHPPSEDRF LHIMEDDSIE EKPLKMKGKD 1500
SSEKKRKRKL EKVEQLFGEG KQKTKELKKI DKPKKKKLKL NVDKSKELNK 1550
LAKKLAKEEE RKKKKEKAAA AKVELVKEST EKKRERKVLD IPSKYDWSGA 1600
EESDDENAVC AAQNCQRPCK DKVDWVQCDG GCDEWFHQVC VGVSAEMAEN 1650
EDYICINCAK KQGPDSPGQA PPPPFLMSYK LPMEDLKETS 1690
Length:1,690
Mass (Da):192,216
Last modified:June 26, 2007 - v2
Checksum:iEFCF56AAAA51F0FC
GO

Sequence cautioni

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 101A → S in BAE38548. 1 Publication
Sequence conflicti14 – 141V → R in BAE38548. 1 Publication
Sequence conflicti17 – 171P → A in BAE38548. 1 Publication
Sequence conflicti24 – 241P → A in BAE38548. 1 Publication
Sequence conflicti544 – 5441V → A in BAE38548. 1 Publication
Sequence conflicti1272 – 12721A → P in BAE22414. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSiCCDS51889.1.
RefSeqiNP_666109.2. NM_145997.2.
UniGeneiMm.404761.
Mm.463658.

Genome annotation databases

EnsembliENSMUST00000100996; ENSMUSP00000098558; ENSMUSG00000030180.
GeneIDi214899.
KEGGimmu:214899.
UCSCiuc009dne.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
CCDSi CCDS51889.1.
RefSeqi NP_666109.2. NM_145997.2.
UniGenei Mm.404761.
Mm.463658.

3D structure databases

ProteinModelPortali Q3UXZ9.
SMRi Q3UXZ9. Positions 18-81, 84-175, 260-585, 1162-1221, 1608-1659.
ModBasei Search...

Protein-protein interaction databases

BioGridi 229572. 1 interaction.
IntActi Q3UXZ9. 1 interaction.

PTM databases

PhosphoSitei Q3UXZ9.

Proteomic databases

PaxDbi Q3UXZ9.
PRIDEi Q3UXZ9.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENSMUST00000100996 ; ENSMUSP00000098558 ; ENSMUSG00000030180 .
GeneIDi 214899.
KEGGi mmu:214899.
UCSCi uc009dne.2. mouse.

Organism-specific databases

CTDi 5927.
MGIi MGI:2136980. Kdm5a.

Phylogenomic databases

eggNOGi NOG327026.
GeneTreei ENSGT00530000063118.
HOGENOMi HOG000290719.
InParanoidi Q3UXZ9.
KOi K11446.
OMAi CVAHYRR.
PhylomeDBi Q3UXZ9.
TreeFami TF106476.

Miscellaneous databases

ChiTaRSi KDM5A. mouse.
NextBioi 374501.
PROi Q3UXZ9.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q3UXZ9.
Bgeei Q3UXZ9.
CleanExi MM_RBP2.
Genevestigatori Q3UXZ9.

Family and domain databases

Gene3Di 1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProi IPR001606. 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 ]
Pfami PF01388. 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 ]
SMARTi SM00501. BRIGHT. 1 hit.
SM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 3 hits.
[Graphical view ]
SUPFAMi SSF46774. SSF46774. 1 hit.
SSF57903. SSF57903. 3 hits.
PROSITEi PS51011. 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 ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.
    , 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. 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].

Entry informationi

Entry nameiKDM5A_MOUSE
AccessioniPrimary (citable) accession number: Q3UXZ9
Secondary accession number(s): Q3TM94, Q3UMI5, Q66JZ3
Entry historyi
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 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