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Q80Y84 (KDM5B_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 96. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 5B

EC=1.14.11.-
Alternative name(s):
Histone demethylase JARID1B
Jumonji/ARID domain-containing protein 1B
PLU-1
Gene names
Name:Kdm5b
Synonyms:Jarid1b, Kiaa4034, Plu1
OrganismMus musculus (Mouse) [Reference proteome]
Taxonomic identifier10090 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus

Protein attributes

Sequence length1544 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone demethylase that demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated, dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional corepressor for FOXG1B and PAX9. Ref.7 Ref.8

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subunit structure

Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7 By similarity.

Subcellular location

Nucleus Ref.6.

Tissue specificity

Present at highest levels in testis, where it is enriched in spermatogonia and pachytene cells (at protein level). Ref.1 Ref.5 Ref.6

Developmental stage

Expressed in developing brain, mammary bud, thymus, teeth, whisker follicle, intervertebral disks, olfactory epithelium, eye, stomach and limbs. Ref.1

Domain

Both the JmjC domain and the JmjN domain are required for enzymatic activity.

The 2 first PHD-type zinc finger domains are required for transcription repression activity By similarity.

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 BAD90482.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DomainRepeat
Zinc-finger
   LigandIron
Metal-binding
Zinc
   Molecular functionChromatin regulator
Dioxygenase
Oxidoreductase
   PTMAcetylation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processhistone H3-K4 demethylation

Inferred from sequence or structural similarity. Source: UniProtKB

negative regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleolus

Inferred from electronic annotation. Source: Ensembl

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

histone demethylase activity (H3-K4 specific)

Inferred from direct assay Ref.7. Source: MGI

histone demethylase activity (H3-dimethyl-K4 specific)

Inferred from sequence or structural similarity. Source: UniProtKB

histone demethylase activity (H3-trimethyl-K4 specific)

Inferred from sequence or structural similarity. 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 PubMed 21448134. Source: IntAct

transcription corepressor activity

Inferred from electronic annotation. Source: Ensembl

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Morf4l1P607624EBI-1249551,EBI-2943018

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q80Y84-1)

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: Q80Y84-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1501-1544: DWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTGKDAPSRK → SEVWAIEDALSPNSETL
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 15441544Lysine-specific demethylase 5B
PRO_0000292413

Regions

Domain32 – 7342JmjN
Domain97 – 18791ARID
Domain453 – 619167JmjC
Zinc finger309 – 35951PHD-type 1
Zinc finger1176 – 122449PHD-type 2
Zinc finger1484 – 153855PHD-type 3

Sites

Metal binding4991Iron; catalytic By similarity
Metal binding5021Iron; catalytic By similarity
Metal binding5871Iron; catalytic By similarity

Amino acid modifications

Modified residue8321N6-acetyllysine Ref.9

Natural variations

Alternative sequence1501 – 154444DWVQC…APSRK → SEVWAIEDALSPNSETL in isoform 2.
VSP_026409

Experimental info

Mutagenesis4991H → A: Abolishes enzymatic activity. Ref.8
Sequence conflict281P → S in BAD90482. Ref.2
Sequence conflict1391E → Q in BAC30898. Ref.4
Sequence conflict7611N → Y in AAL92848. Ref.1
Sequence conflict7611N → Y in AAL92849. Ref.1
Sequence conflict14281K → R in AAL92848. Ref.1
Sequence conflict14281K → R in AAL92849. Ref.1

Secondary structure

................ 1544
Helix Strand Turn

Details...

Sequences

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

Last modified June 1, 2003. Version 1.
Checksum: D83E2691C65DCB31

FASTA1,544175,555
        10         20         30         40         50         60 
MEPATTLPPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH KIRPIAEQTG 

        70         80         90        100        110        120 
ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK LNFLDQIAKY WELQGSTLKI 

       130        140        150        160        170        180 
PHVERKILDL FQLNKLVAEE GGFAVVCKDR KWTKIATKMG FAPGKAVGSH IRGHYERILN 

       190        200        210        220        230        240 
PYNLFLSGDS LRCLQKPNLT SDTKDKEYKP HDIPQRQSVQ PAETCPPARR AKRMRAEAMN 

       250        260        270        280        290        300 
IKIEPEEATE ARTHNLRRRM GCTTPKWENE KEMKSTIKQE PTEKKDCELE SEKEKPKSRA 

       310        320        330        340        350        360 
KKTATAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLV PPLHDVPKGD WRCPKCLAQE 

       370        380        390        400        410        420 
CNKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM VPTELVEKEF WRLVSTIEED 

       430        440        450        460        470        480 
VTVEYGADIA SKEFGSGFPV RDGKIKISPE EEEYLDSGWN LNNMPVMEQS VLAHITADIC 

       490        500        510        520        530        540 
GMKLPWLYVG MCFSSFCWHI EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE 

       550        560        570        580        590        600 
LFVSQPDLLH QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV 

       610        620        630        640        650        660 
NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST VQKDMAIMIE 

       670        680        690        700        710        720 
DEKALRETVR KLGVIDSERM DFELLPDDER QCIKCKTTCF MSAISCSCKP GLLVCLHHVK 

       730        740        750        760        770        780 
ELCSCPPYKY NLRYRYTLDD LYPMMNALKL RAESYNEWAL NVNEALEAKI NKKKSLVSFK 

       790        800        810        820        830        840 
ALIEESEMKK FPDNDLLRHL RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN 

       850        860        870        880        890        900 
ELRQFVTQLY ALPCVLSQTP LLKDLLNRVE DFQQQSQKLL SEEMPSAAEL QELLDVSFEF 

       910        920        930        940        950        960 
DVELPQLTEM RIRLEQARWL EEVQQACLDS SSLSLDDMRR LIDLGVGLAP YSAVEKAMAR 

       970        980        990       1000       1010       1020 
LQELLTVSEH WDDKAKSLLR ARPRHSLSSL ATAVKEMEEI PAYLPNGTVL KDSVQRARDW 

      1030       1040       1050       1060       1070       1080 
VQDVDALQAG GRVPVLETLI ELVARGRSIP VHLNSLPRLE MLVAEVHAWK ECAAKTFLPE 

      1090       1100       1110       1120       1130       1140 
NSTYSLLEVL CPRCDIGLLG LKRKQRKLKE PLPSGKKRST KLESLSDLER ALMESKETAA 

      1150       1160       1170       1180       1190       1200 
AMATLGEARL REMEALQSLR FANEEKLLSP VQDLEMKVCL CQKTPATPMI QCELCRDAFH 

      1210       1220       1230       1240       1250       1260 
TSCVAAPSIS QSSRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD ALRYMIERTV 

      1270       1280       1290       1300       1310       1320 
NWQHRAQQLL SSGNLKLVQD QVGSGLLSSR WPASAGQASA TDKVSQPPGT TSFSLPDDWD 

      1330       1340       1350       1360       1370       1380 
NRTSYLHSPF STGQSCLPLH GLSPEVNELL MEAQLLQVSL PEIQELYQTL LTKPSSVQQA 

      1390       1400       1410       1420       1430       1440 
DRSSPVRSSS EKNDCLRGKR DAINSPERKL KRRPEREGLP SERWDRVKHM RTPQKKKIKL 

      1450       1460       1470       1480       1490       1500 
SHPKDMDSFK LERERSYDLV RNAETHSLPS DTSYSEQEDS EDEDAICPAV SCLQPEGDEV 

      1510       1520       1530       1540 
DWVQCDGSCN QWFHQVCVGV SPEMAEKEDY ICVRCTGKDA PSRK 

« Hide

Isoform 2 [UniParc].

Checksum: 37772163EC76CDB2
Show »

FASTA1,517172,410

References

« Hide 'large scale' references
[1]"Characterisation and developmental expression of mouse Plu-1, a homologue of a human nuclear protein (PLU-1) which is specifically up-regulated in breast cancer."
Madsen B., Spencer-Dene B., Poulsom R., Hall D., Lu P.J., Scott K., Shaw A.T., Burchell J.M., Freemont P., Taylor-Papadimitriou J.
Mech. Dev. 119:S239-S246(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, DEVELOPMENTAL STAGE.
Strain: BALB/c.
Tissue: Testis.
[2]"Prediction of the coding sequences of mouse homologues of KIAA gene. The complete nucleotide sequences of mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
Okazaki N., Kikuno R.F., Ohara R., Inamoto S., Nagase T., Ohara O., Koga H.
Submitted (FEB-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Brain.
[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] (ISOFORM 1).
Strain: C57BL/6.
Tissue: Brain.
[4]"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 1-1433.
Strain: C57BL/6J.
Tissue: Aorta.
[5]"PLU-1 nuclear protein, which is upregulated in breast cancer, shows restricted expression in normal human adult tissues: a new cancer/testis antigen?"
Barrett A., Madsen B., Copier J., Lu P.J., Cooper L., Scibetta A.G., Burchell J., Taylor-Papadimitriou J.
Int. J. Cancer 101:581-588(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY.
[6]"PLU-1, a transcriptional repressor and putative testis-cancer antigen, has a specific expression and localisation pattern during meiosis."
Madsen B., Tarsounas M., Burchell J.M., Hall D., Poulsom R., Taylor-Papadimitriou J.
Chromosoma 112:124-132(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: TISSUE SPECIFICITY, SUBCELLULAR LOCATION.
[7]"The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases."
Iwase S., Lan F., Bayliss P., de la Torre-Ubieta L., Huarte M., Qi H.H., Whetstine J.R., Bonni A., Roberts T.M., Shi Y.
Cell 128:1077-1088(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins."
Seward D.J., Cubberley G., Kim S., Schonewald M., Zhang L., Tripet B., Bentley D.L.
Nat. Struct. Mol. Biol. 14:240-242(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF HIS-499.
[9]"SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways."
Park J., Chen Y., Tishkoff D.X., Peng C., Tan M., Dai L., Xie Z., Zhang Y., Zwaans B.M., Skinner M.E., Lombard D.B., Zhao Y.
Mol. Cell 50:919-930(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-832, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Embryonic fibroblast.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AY082429 mRNA. Translation: AAL92848.1.
AY082430 mRNA. Translation: AAL92849.1.
AK220451 mRNA. Translation: BAD90482.1. Different initiation.
BC048180 mRNA. Translation: AAH48180.1.
BC057318 mRNA. Translation: AAH57318.1.
AK041304 mRNA. Translation: BAC30898.1.
CCDSCCDS35716.1. [Q80Y84-1]
RefSeqNP_690855.2. NM_152895.2. [Q80Y84-1]
UniGeneMm.28995.
Mm.391994.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2EQYNMR-A94-208[»]
DisProtDP00711.
ProteinModelPortalQ80Y84.
SMRQ80Y84. Positions 31-208, 310-601, 1177-1227, 1486-1544.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid217610. 3 interactions.
IntActQ80Y84. 4 interactions.

PTM databases

PhosphoSiteQ80Y84.

Proteomic databases

MaxQBQ80Y84.
PaxDbQ80Y84.
PRIDEQ80Y84.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENSMUST00000047714; ENSMUSP00000038138; ENSMUSG00000042207. [Q80Y84-1]
ENSMUST00000112198; ENSMUSP00000107817; ENSMUSG00000042207. [Q80Y84-2]
GeneID75605.
KEGGmmu:75605.
UCSCuc007csg.2. mouse. [Q80Y84-2]
uc011wsg.1. mouse. [Q80Y84-1]

Organism-specific databases

CTD10765.
MGIMGI:1922855. Kdm5b.
RougeSearch...

Phylogenomic databases

eggNOGNOG327026.
GeneTreeENSGT00530000063118.
HOGENOMHOG000290719.
InParanoidQ80Y84.
KOK11446.
OMAPHSSVER.
OrthoDBEOG7D85VK.
PhylomeDBQ80Y84.
TreeFamTF106476.

Gene expression databases

ArrayExpressQ80Y84.
BgeeQ80Y84.
GenevestigatorQ80Y84.

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. 3 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

EvolutionaryTraceQ80Y84.
NextBio343484.
PROQ80Y84.
SOURCESearch...

Entry information

Entry nameKDM5B_MOUSE
AccessionPrimary (citable) accession number: Q80Y84
Secondary accession number(s): Q5DTR9, Q8BLU1, Q8JZL8
Entry history
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: June 1, 2003
Last modified: July 9, 2014
This is version 96 of the entry and version 1 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

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MGD cross-references

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