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Protein

Lysine-specific demethylase 5B

Gene

Kdm5b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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
Metal bindingi499Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi502Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi587Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri309 – 359PHD-type 1PROSITE-ProRule annotationAdd BLAST51
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
  • histone H3-K4 demethylation Source: UniProtKB
  • 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
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase, Repressor

Keywords - Biological processi

Biological rhythms, Transcription, Transcription regulation

Keywords - Ligandi

Iron, 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 1

Organism-specific databases

MGIiMGI:1922855. Kdm5b.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

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-linki242Glycyl 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
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.By similarity

Binary interactionsi

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

Protein-protein interaction databases

BioGridi217610. 3 interactors.
IntActiQ80Y84. 4 interactors.
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[»]
DisProtiDP00711.
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.
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
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 fingeri309 – 359PHD-type 1PROSITE-ProRule annotationAdd BLAST51
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.
OMAiNECCRGK.
OrthoDBiEOG091G0RFR.
PhylomeDBiQ80Y84.
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. 3 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]

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

Cross-referencesi

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.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2EQYNMR-A94-208[»]
DisProtiDP00711.
ProteinModelPortaliQ80Y84.
SMRiQ80Y84.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

PTM databases

iPTMnetiQ80Y84.
PhosphoSitePlusiQ80Y84.

Proteomic databases

PaxDbiQ80Y84.
PeptideAtlasiQ80Y84.
PRIDEiQ80Y84.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]

Organism-specific databases

CTDi10765.
MGIiMGI:1922855. Kdm5b.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00530000063118.
HOGENOMiHOG000290719.
InParanoidiQ80Y84.
KOiK11446.
OMAiNECCRGK.
OrthoDBiEOG091G0RFR.
PhylomeDBiQ80Y84.
TreeFamiTF106476.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiQ80Y84.
PROiQ80Y84.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000042207.
GenevisibleiQ80Y84. 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. 3 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 nameiKDM5B_MOUSE
AccessioniPrimary (citable) accession number: Q80Y84
Secondary accession number(s): Q5DTR9, Q8BLU1, Q8JZL8
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: June 1, 2003
Last modified: November 2, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. 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.