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Protein

Lysine-specific demethylase 5B

Gene

Kdm5b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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. Represses the CLOCK-ARNTL/BMAL1 heterodimer-mediated transcriptional activation of the core clock component PER2.3 Publications

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei4252-oxoglutarateBy similarity1
Metal bindingi499Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi501Iron; catalyticBy similarity1
Binding sitei5072-oxoglutarateBy similarity1
Binding sitei5092-oxoglutarateBy similarity1
Binding sitei5172-oxoglutarateBy similarity1
Metal bindingi587Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri309 – 359PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri692 – 744C5HC2By similarityAdd BLAST53
Zinc fingeri1176 – 1224PHD-type 2PROSITE-ProRule annotationAdd BLAST49
Zinc fingeri1484 – 1538PHD-type 3PROSITE-ProRule annotationAdd BLAST55

GO - Molecular functioni

GO - Biological processi

  • branching involved in mammary gland duct morphogenesis Source: MGI
  • cellular response to fibroblast growth factor stimulus Source: Ensembl
  • cellular response to leukemia inhibitory factor Source: MGI
  • histone H3-K4 demethylation Source: MGI
  • lens fiber cell differentiation Source: Ensembl
  • mammary duct terminal end bud growth Source: MGI
  • negative regulation of transcription, DNA-templated Source: UniProtKB
  • positive regulation of gene expression Source: MGI
  • positive regulation of mammary gland epithelial cell proliferation Source: MGI
  • post-embryonic development Source: MGI
  • regulation of circadian rhythm Source: UniProtKB
  • regulation of estradiol secretion Source: MGI
  • response to fungicide Source: Ensembl
  • rhythmic process Source: UniProtKB-KW
  • single fertilization Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
  • uterus morphogenesis Source: MGI

Keywordsi

Molecular functionChromatin regulator, Dioxygenase, Oxidoreductase, Repressor
Biological processBiological rhythms, Transcription, Transcription regulation
LigandIron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-3214842 HDMs demethylate histones
R-MMU-8866911 TFAP2 (AP-2) family regulates transcription of cell cycle factors

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 5B (EC:1.14.11.-)
Alternative name(s):
Histone demethylase JARID1B
Jumonji/ARID domain-containing protein 1B
PLU-1
Gene namesi
Name:Kdm5b
Synonyms:Jarid1b, Kiaa4034, Plu1
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:1922855 Kdm5b

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi499H → A: Abolishes enzymatic activity. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002924131 – 1544Lysine-specific demethylase 5BAdd BLAST1544

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Cross-linki148Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki204Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki209Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki242Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki274Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki278Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Cross-linki769Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei832N6-acetyllysineCombined sources1
Modified residuei986PhosphoserineBy similarity1
Modified residuei1328PhosphoserineBy similarity1
Cross-linki1450Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)By similarity
Modified residuei1456PhosphoserineBy similarity1

Keywords - PTMi

Acetylation, Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

PaxDbiQ80Y84
PeptideAtlasiQ80Y84
PRIDEiQ80Y84

PTM databases

iPTMnetiQ80Y84
PhosphoSitePlusiQ80Y84

Expressioni

Tissue specificityi

Present at highest levels in testis, where it is enriched in spermatogonia and pachytene cells (at protein level).3 Publications

Developmental stagei

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

Gene expression databases

BgeeiENSMUSG00000042207
GenevisibleiQ80Y84 MM

Interactioni

Subunit structurei

Interacts with FOXG1B, PAX9, MYC, MYCN and RB1. Interacts with HDAC1, HDAC4, HDAC5 and HDAC7. Interacts (via PHD-type 1 zinc finger) with histone H3 unmodified at 'Lys-4'; the interaction is inhibited when histone H3 is methylated at 'Arg-2' or 'Lys-4' (By similarity).By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
Morf4l1P607624EBI-1249551,EBI-2943018

GO - Molecular functioni

Protein-protein interaction databases

BioGridi217610, 3 interactors
IntActiQ80Y84, 4 interactors
MINTiQ80Y84
STRINGi10090.ENSMUSP00000038138

Structurei

Secondary structure

11544
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi97 – 114Combined sources18
Beta strandi122 – 127Combined sources6
Helixi130 – 140Combined sources11
Helixi143 – 148Combined sources6
Turni149 – 151Combined sources3
Helixi152 – 158Combined sources7
Beta strandi163 – 165Combined sources3
Helixi166 – 177Combined sources12
Helixi179 – 187Combined sources9

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2EQYNMR-A94-208[»]
ProteinModelPortaliQ80Y84
SMRiQ80Y84
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ80Y84

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini32 – 73JmjNPROSITE-ProRule annotationAdd BLAST42
Domaini97 – 187ARIDPROSITE-ProRule annotationAdd BLAST91
Domaini453 – 619JmjCPROSITE-ProRule annotationAdd BLAST167

Domaini

Both the JmjC domain and the JmjN domain are required for enzymatic activity. However ARID and PHD-type 1 domain are not required for activity per se but contributed to recognition of the H3(1-21)K4me2 substrate peptide.By similarity
The 2 first PHD-type zinc finger domains are required for transcription repression activity.By similarity

Sequence similaritiesi

Belongs to the JARID1 histone demethylase family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri309 – 359PHD-type 1PROSITE-ProRule annotationAdd BLAST51
Zinc fingeri692 – 744C5HC2By similarityAdd BLAST53
Zinc fingeri1176 – 1224PHD-type 2PROSITE-ProRule annotationAdd BLAST49
Zinc fingeri1484 – 1538PHD-type 3PROSITE-ProRule annotationAdd BLAST55

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1246 Eukaryota
ENOG410XR9J LUCA
GeneTreeiENSGT00530000063118
HOGENOMiHOG000290719
InParanoidiQ80Y84
KOiK11446
OMAiCKTTCFM
OrthoDBiEOG091G0RFR
PhylomeDBiQ80Y84
TreeFamiTF106476

Family and domain databases

Gene3Di1.10.150.60, 1 hit
3.30.40.10, 2 hits
InterProiView protein in InterPro
IPR001606 ARID_dom
IPR036431 ARID_dom_sf
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
PfamiView protein in Pfam
PF01388 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
SMARTiView protein in SMART
SM00501 BRIGHT, 1 hit
SM00558 JmjC, 1 hit
SM00545 JmjN, 1 hit
SM00249 PHD, 3 hits
SUPFAMiSSF46774 SSF46774, 1 hit
SSF57903 SSF57903, 3 hits
PROSITEiView protein in PROSITE
PS51011 ARID, 1 hit
PS51184 JMJC, 1 hit
PS51183 JMJN, 1 hit
PS01359 ZF_PHD_1, 2 hits
PS50016 ZF_PHD_2, 3 hits

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q80Y84-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MEPATTLPPG PRPALPLGGP GPLGEFLPPP ECPVFEPSWE EFADPFAFIH
60 70 80 90 100
KIRPIAEQTG ICKVRPPPDW QPPFACDVDK LHFTPRIQRL NELEAQTRVK
110 120 130 140 150
LNFLDQIAKY WELQGSTLKI PHVERKILDL FQLNKLVAEE GGFAVVCKDR
160 170 180 190 200
KWTKIATKMG FAPGKAVGSH IRGHYERILN PYNLFLSGDS LRCLQKPNLT
210 220 230 240 250
SDTKDKEYKP HDIPQRQSVQ PAETCPPARR AKRMRAEAMN IKIEPEEATE
260 270 280 290 300
ARTHNLRRRM GCTTPKWENE KEMKSTIKQE PTEKKDCELE SEKEKPKSRA
310 320 330 340 350
KKTATAVDLY VCLLCGSGND EDRLLLCDGC DDSYHTFCLV PPLHDVPKGD
360 370 380 390 400
WRCPKCLAQE CNKPQEAFGF EQAARDYTLR TFGEMADAFK SDYFNMPVHM
410 420 430 440 450
VPTELVEKEF WRLVSTIEED VTVEYGADIA SKEFGSGFPV RDGKIKISPE
460 470 480 490 500
EEEYLDSGWN LNNMPVMEQS VLAHITADIC GMKLPWLYVG MCFSSFCWHI
510 520 530 540 550
EDHWSYSINY LHWGEPKTWY GVPGYAAEQL ENVMKKLAPE LFVSQPDLLH
560 570 580 590 600
QLVTIMNPNT LMTHEVPVYR TNQCAGEFVI TFPRAYHSGF NQGFNFAEAV
610 620 630 640 650
NFCTVDWLPL GRQCVEHYRL LHRYCVFSHD EMICKMASKA DVLDVVVAST
660 670 680 690 700
VQKDMAIMIE DEKALRETVR KLGVIDSERM DFELLPDDER QCIKCKTTCF
710 720 730 740 750
MSAISCSCKP GLLVCLHHVK ELCSCPPYKY NLRYRYTLDD LYPMMNALKL
760 770 780 790 800
RAESYNEWAL NVNEALEAKI NKKKSLVSFK ALIEESEMKK FPDNDLLRHL
810 820 830 840 850
RLVTQDAEKC ASVAQQLLNG KRQTRYRSGG GKSQNQLTVN ELRQFVTQLY
860 870 880 890 900
ALPCVLSQTP LLKDLLNRVE DFQQQSQKLL SEEMPSAAEL QELLDVSFEF
910 920 930 940 950
DVELPQLTEM RIRLEQARWL EEVQQACLDS SSLSLDDMRR LIDLGVGLAP
960 970 980 990 1000
YSAVEKAMAR LQELLTVSEH WDDKAKSLLR ARPRHSLSSL ATAVKEMEEI
1010 1020 1030 1040 1050
PAYLPNGTVL KDSVQRARDW VQDVDALQAG GRVPVLETLI ELVARGRSIP
1060 1070 1080 1090 1100
VHLNSLPRLE MLVAEVHAWK ECAAKTFLPE NSTYSLLEVL CPRCDIGLLG
1110 1120 1130 1140 1150
LKRKQRKLKE PLPSGKKRST KLESLSDLER ALMESKETAA AMATLGEARL
1160 1170 1180 1190 1200
REMEALQSLR FANEEKLLSP VQDLEMKVCL CQKTPATPMI QCELCRDAFH
1210 1220 1230 1240 1250
TSCVAAPSIS QSSRIWLCPH CRRSEKPPLE KILPLLASLQ RIRVRLPEGD
1260 1270 1280 1290 1300
ALRYMIERTV NWQHRAQQLL SSGNLKLVQD QVGSGLLSSR WPASAGQASA
1310 1320 1330 1340 1350
TDKVSQPPGT TSFSLPDDWD NRTSYLHSPF STGQSCLPLH GLSPEVNELL
1360 1370 1380 1390 1400
MEAQLLQVSL PEIQELYQTL LTKPSSVQQA DRSSPVRSSS EKNDCLRGKR
1410 1420 1430 1440 1450
DAINSPERKL KRRPEREGLP SERWDRVKHM RTPQKKKIKL SHPKDMDSFK
1460 1470 1480 1490 1500
LERERSYDLV RNAETHSLPS DTSYSEQEDS EDEDAICPAV SCLQPEGDEV
1510 1520 1530 1540
DWVQCDGSCN QWFHQVCVGV SPEMAEKEDY ICVRCTGKDA PSRK
Length:1,544
Mass (Da):175,555
Last modified:June 1, 2003 - v1
Checksum:iD83E2691C65DCB31
GO
Isoform 2 (identifier: Q80Y84-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1501-1544: DWVQCDGSCNQWFHQVCVGVSPEMAEKEDYICVRCTGKDAPSRK → SEVWAIEDALSPNSETL

Note: No experimental confirmation available.
Show »
Length:1,517
Mass (Da):172,410
Checksum:i37772163EC76CDB2
GO

Sequence cautioni

The sequence BAD90482 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti28P → S in BAD90482 (Ref. 2) Curated1
Sequence conflicti139E → Q in BAC30898 (PubMed:16141072).Curated1
Sequence conflicti761N → Y in AAL92848 (PubMed:14516692).Curated1
Sequence conflicti761N → Y in AAL92849 (PubMed:14516692).Curated1
Sequence conflicti1428K → R in AAL92848 (PubMed:14516692).Curated1
Sequence conflicti1428K → R in AAL92849 (PubMed:14516692).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0264091501 – 1544DWVQC…APSRK → SEVWAIEDALSPNSETL in isoform 2. 1 PublicationAdd BLAST44

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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
CCDSiCCDS35716.1 [Q80Y84-1]
RefSeqiNP_690855.2, NM_152895.2 [Q80Y84-1]
UniGeneiMm.28995
Mm.391994

Genome annotation databases

EnsembliENSMUST00000047714; ENSMUSP00000038138; ENSMUSG00000042207 [Q80Y84-1]
ENSMUST00000112198; ENSMUSP00000107817; ENSMUSG00000042207 [Q80Y84-2]
GeneIDi75605
KEGGimmu:75605
UCSCiuc007csg.2 mouse [Q80Y84-2]
uc011wsg.1 mouse [Q80Y84-1]

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiKDM5B_MOUSE
AccessioniPrimary (citable) accession number: Q80Y84
Secondary accession number(s): Q5DTR9, Q8BLU1, Q8JZL8
Entry historyiIntegrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: June 1, 2003
Last modified: March 28, 2018
This is version 127 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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