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Protein

Lysine-specific demethylase 5A

Gene

Kdm5a

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: 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. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1.3 Publications

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi483Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi486Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi571Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri293 – 343PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1153 – 1210PHD-type 2PROSITE-ProRule annotationAdd BLAST58
Zinc fingeri1599 – 1653PHD-type 3PROSITE-ProRule annotationAdd BLAST55

GO - Molecular functioni

GO - Biological processi

  • circadian regulation of gene expression Source: UniProtKB
  • histone H3-K4 demethylation Source: MGI
  • male gonad development Source: Ensembl
  • negative regulation of histone deacetylase activity Source: UniProtKB
  • negative regulation of transcription from RNA polymerase II promoter Source: MGI
  • positive regulation of transcription, DNA-templated Source: MGI
  • spermatogenesis Source: Ensembl
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Chromatin regulator, Developmental protein, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

BRENDAi1.14.11.B2. 3474.
ReactomeiR-MMU-3214842. HDMs demethylate histones.

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
Proteomesi
  • UP000000589 Componenti: Chromosome 6

Organism-specific databases

MGIiMGI:2136980. Kdm5a.

Subcellular locationi

  • Nucleusnucleolus By similarity
  • Nucleus PROSITE-ProRule annotation1 Publication

  • Note: Occupies promoters of genes involved in RNA metabolism and mitochondrial function.1 Publication

GO - Cellular componenti

  • cyclin-dependent protein kinase activating kinase holoenzyme complex Source: Ensembl
  • cytoplasm Source: MGI
  • nucleolus Source: UniProtKB-SubCell
  • nucleus Source: MGI
  • protein-DNA complex Source: MGI
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)DescriptionActionsGraphical viewLength
ChainiPRO_00002924111 – 1690Lysine-specific demethylase 5AAdd BLAST1690

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei204PhosphoserineBy similarity1
Modified residuei1111PhosphoserineCombined sources1
Modified residuei1330PhosphoserineBy similarity1
Modified residuei1331PhosphoserineBy similarity1
Modified residuei1343PhosphothreonineCombined sources1
Modified residuei1345PhosphoserineCombined sources1
Modified residuei1438PhosphoserineBy similarity1
Modified residuei1488PhosphoserineBy similarity1
Modified residuei1595PhosphotyrosineCombined sources1
Modified residuei1598PhosphoserineCombined sources1
Modified residuei1603PhosphoserineCombined sources1
Modified residuei1666PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ3UXZ9.
MaxQBiQ3UXZ9.
PaxDbiQ3UXZ9.
PeptideAtlasiQ3UXZ9.
PRIDEiQ3UXZ9.

PTM databases

iPTMnetiQ3UXZ9.
PhosphoSitePlusiQ3UXZ9.

Expressioni

Gene expression databases

BgeeiENSMUSG00000030180.
CleanExiMM_RBP2.
ExpressionAtlasiQ3UXZ9. baseline and differential.
GenevisibleiQ3UXZ9. MM.

Interactioni

Subunit structurei

Interacts with RB1, ESR1, MYC, MYCN and LMO2 (By similarity). Interacts with SUZ12; the interaction is direct. Interacts with HDAC1, ARNTL/BMAL1 and CLOCK.By similarity2 Publications

Binary interactionsi

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

Protein-protein interaction databases

BioGridi229572. 6 interactors.
IntActiQ3UXZ9. 6 interactors.
STRINGi10090.ENSMUSP00000098558.

Chemistry databases

BindingDBiQ3UXZ9.

Structurei

3D structure databases

ProteinModelPortaliQ3UXZ9.
SMRiQ3UXZ9.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini19 – 60JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini84 – 174ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini437 – 603JmjCPROSITE-ProRule annotationAdd BLAST167

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni1622 – 1690Interaction with LMO2By similarityAdd BLAST69

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi419 – 423GSGFP motif1 Publication5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi1484 – 1579Lys-richAdd BLAST96

Domaini

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

Sequence similaritiesi

Belongs to the JARID1 histone demethylase family.Curated
Contains 1 ARID domain.PROSITE-ProRule annotation
Contains 1 JmjC domain.PROSITE-ProRule annotation
Contains 1 JmjN domain.PROSITE-ProRule annotation
Contains 3 PHD-type zinc fingers.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri293 – 343PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri1153 – 1210PHD-type 2PROSITE-ProRule annotationAdd BLAST58
Zinc fingeri1599 – 1653PHD-type 3PROSITE-ProRule annotationAdd BLAST55

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
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_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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

        10         20         30         40         50
MASVGPGGYA AEFVPPPECP VFEPSWEEFT DPLSFIGRIR PFAEKTGICK
60 70 80 90 100
IRPPKDWQPP FACEVKTFRF TPRVQRLNEL EAMTRVRLDF LDQLAKFWEL
110 120 130 140 150
QGSTLKIPVV ERKILDLYAL SKIVASKGGF EIVTKEKKWS KVGSRLGYLP
160 170 180 190 200
GKGTGSLLKS HYERILYPYE LFQSGVSLMG VQMPDLDLKE KVEAEVLSTD
210 220 230 240 250
IQPSPERGTR MNIPPKRTRR VKSQSDSGEV NRNTELKKLQ IFGAGPKVVG
260 270 280 290 300
LAVGAKDKED EVTRRRKVTN RSDAFNMQMR QRKGTLSVNF VDLYVCMFCG
310 320 330 340 350
RGNNEDKLLL CDGCDDSYHT FCLLPPLPDV PKGDWRCPKC VAEECNKPRE
360 370 380 390 400
AFGFEQAVRE YTLQSFGEMA DNFKSDYFNM PVHMVPTELV EKEFWRLVSS
410 420 430 440 450
IEEDVIVEYG ADISSKDFGS GFPKKDGQRK MLPEEEEYAL SGWNLNNMPV
460 470 480 490 500
LEQSVLAHIN VDISGMKVPW LYVGMCFSSF CWHIEDHWSY SINYLHWGEP
510 520 530 540 550
KTWYGVPSHA AEQLEEVMRE LAPELFESQP DLLHQLVTIM NPNVLMEHGV
560 570 580 590 600
PVYRTNQCAG EFVVTFPRAY HSGFNQGYNF AEAVNFCTAD WLPIGRQCVN
610 620 630 640 650
HYRRLRRHCV FSHEELIFKM AADPECLDVG LAAMVCKELT LMTEEETRLR
660 670 680 690 700
ESVVQMGVVM SEEEVFELVP DDERQCSACR TTCFLSALTC SCNPERLVCL
710 720 730 740 750
YHPTDLCSCP MQNKCLRYRY PLEDLPSLLY GVKVRAQSYD TWVNRVTEAL
760 770 780 790 800
SASFNHKKDL IELRVMLEDA EDRKYPENDL FRKLRDAVKE AETCGSVAQL
810 820 830 840 850
LLSKKQKHRQ SSDSGKTRTK LTVEELKAFV QQLVSLPCVI SQTRQVKNLL
860 870 880 890 900
DDVEEFHERA QEAMMDETPD SSKLQMLIDM GSSLYVELPE LPRLKQELQQ
910 920 930 940 950
ARWLDEVRLT LSDPQQVTLD VMKKLIDSGV GLAPHHAVEK AMAELQELLT
960 970 980 990 1000
VSERWEEKAK VCLQARPRHS MANLENIVNE AKNIPAFLPN VLSLKEALQK
1010 1020 1030 1040 1050
AREWTAKVEA IQSGNNYAYL EQLESLSAKG RPIPVRLDAL PQVESQVAAA
1060 1070 1080 1090 1100
RAWRERTGRT FLKKNSSHTL LQVLSPRTDI GVYGSGKNRR KKVKEIIEKE
1110 1120 1130 1140 1150
KEKDLDLEPL SDLEEGLEES RDTAMVVAVF KEREQKEIEA MHSLRAANLA
1160 1170 1180 1190 1200
KMTIVERIEE VKFCICRKTA SGFMLQCELC KDWFHNSCVP LPKSSSQKKG
1210 1220 1230 1240 1250
SSWQAKDVKF LCPLCMRSRR PRLETILSLL VSLQKLPVRL PEGEALQCLT
1260 1270 1280 1290 1300
ERAMSWQDKA RQALATDELS SALAKLSVLS QRMVEQAARE KTEKIISAEL
1310 1320 1330 1340 1350
QKAAANPDLQ GHLPSFQQSA FNRVVSSVSS SPHQTMDYDD EETDSDEDIR
1360 1370 1380 1390 1400
ETYGYDMKDT ASVKSSSSLE PNLFCDEEIP IKSEEVVTHM WTAPSFCAEH
1410 1420 1430 1440 1450
AYSSASKSCS QGSSTPRKQP RKSPLVPRSL EPPVLELSPG AKAQLEELMM
1460 1470 1480 1490 1500
VGDLLEVSLD ETQHIWRILQ ATHPPSEDRF LHIMEDDSIE EKPLKMKGKD
1510 1520 1530 1540 1550
SSEKKRKRKL EKVEQLFGEG KQKTKELKKI DKPKKKKLKL NVDKSKELNK
1560 1570 1580 1590 1600
LAKKLAKEEE RKKKKEKAAA AKVELVKEST EKKRERKVLD IPSKYDWSGA
1610 1620 1630 1640 1650
EESDDENAVC AAQNCQRPCK DKVDWVQCDG GCDEWFHQVC VGVSAEMAEN
1660 1670 1680 1690
EDYICINCAK KQGPDSPGQA PPPPFLMSYK LPMEDLKETS
Length:1,690
Mass (Da):192,216
Last modified:June 26, 2007 - v2
Checksum:iEFCF56AAAA51F0FC
GO

Sequence cautioni

The sequence BAE22414 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti10A → S in BAE38548 (PubMed:16141072).Curated1
Sequence conflicti14V → R in BAE38548 (PubMed:16141072).Curated1
Sequence conflicti17P → A in BAE38548 (PubMed:16141072).Curated1
Sequence conflicti24P → A in BAE38548 (PubMed:16141072).Curated1
Sequence conflicti544V → A in BAE38548 (PubMed:16141072).Curated1
Sequence conflicti1272A → P in BAE22414 (PubMed:16141072).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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

EnsembliENSMUST00000005108; ENSMUSP00000005108; ENSMUSG00000030180.
GeneIDi214899.
KEGGimmu:214899.
UCSCiuc009dne.2. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.

3D structure databases

ProteinModelPortaliQ3UXZ9.
SMRiQ3UXZ9.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi229572. 6 interactors.
IntActiQ3UXZ9. 6 interactors.
STRINGi10090.ENSMUSP00000098558.

Chemistry databases

BindingDBiQ3UXZ9.

PTM databases

iPTMnetiQ3UXZ9.
PhosphoSitePlusiQ3UXZ9.

Proteomic databases

EPDiQ3UXZ9.
MaxQBiQ3UXZ9.
PaxDbiQ3UXZ9.
PeptideAtlasiQ3UXZ9.
PRIDEiQ3UXZ9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000005108; ENSMUSP00000005108; ENSMUSG00000030180.
GeneIDi214899.
KEGGimmu:214899.
UCSCiuc009dne.2. mouse.

Organism-specific databases

CTDi5927.
MGIiMGI:2136980. Kdm5a.

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ3UXZ9.
KOiK11446.
OMAiCVAHYRR.
PhylomeDBiQ3UXZ9.
TreeFamiTF106476.

Enzyme and pathway databases

BRENDAi1.14.11.B2. 3474.
ReactomeiR-MMU-3214842. HDMs demethylate histones.

Miscellaneous databases

ChiTaRSiKdm5a. mouse.
PROiQ3UXZ9.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000030180.
CleanExiMM_RBP2.
ExpressionAtlasiQ3UXZ9. baseline and differential.
GenevisibleiQ3UXZ9. MM.

Family and domain databases

Gene3Di1.10.150.60. 1 hit.
3.30.40.10. 3 hits.
InterProiIPR001606. ARID_dom.
IPR003347. JmjC_dom.
IPR003349. JmjN.
IPR013637. Lys_sp_deMease-like_dom.
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]
ProtoNetiSearch...

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: November 2, 2016
This is version 104 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.