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Protein

Lysine-specific demethylase 6B

Gene

Kdm6b

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-27' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation.1 Publication

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1388IronBy similarity1
Metal bindingi1390IronBy similarity1
Metal bindingi1468IronBy similarity1
Metal bindingi1573ZincBy similarity1
Metal bindingi1576ZincBy similarity1
Metal bindingi1600ZincBy similarity1
Metal bindingi1603ZincBy similarity1

GO - Molecular functioni

  • beta-catenin binding Source: BHF-UCL
  • chromatin binding Source: Ensembl
  • dioxygenase activity Source: UniProtKB-KW
  • histone demethylase activity (H3-K27 specific) Source: BHF-UCL
  • metal ion binding Source: UniProtKB-KW
  • sequence-specific DNA binding Source: MGI

GO - Biological processi

  • cardiac muscle cell differentiation Source: BHF-UCL
  • cell fate commitment Source: MGI
  • cellular response to hydrogen peroxide Source: MGI
  • endothelial cell differentiation Source: BHF-UCL
  • hippocampus development Source: Ensembl
  • histone demethylation Source: MGI
  • histone H3-K27 demethylation Source: BHF-UCL
  • inflammatory response to antigenic stimulus Source: Ensembl
  • mesodermal cell differentiation Source: BHF-UCL
  • positive regulation of transcription from RNA polymerase II promoter Source: BHF-UCL
  • regulation of gene expression Source: MGI
  • response to activity Source: Ensembl
  • response to fungicide Source: Ensembl
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Inflammatory response

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-2559580. Oxidative Stress Induced Senescence.
R-MMU-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 6B (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing protein 3
Jumonji domain-containing protein 3
Gene namesi
Name:Kdm6b
Synonyms:Jmjd3, Kiaa0346
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 11

Organism-specific databases

MGIiMGI:2448492. Kdm6b.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: BHF-UCL
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002920081 – 1641Lysine-specific demethylase 6BAdd BLAST1641

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei224PhosphoserineBy similarity1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiQ5NCY0.
PaxDbiQ5NCY0.
PeptideAtlasiQ5NCY0.
PRIDEiQ5NCY0.

PTM databases

iPTMnetiQ5NCY0.
PhosphoSitePlusiQ5NCY0.

Expressioni

Inductioni

By inflammatory stimuli; mediated by NF-kappa-B.1 Publication

Gene expression databases

BgeeiENSMUSG00000018476.
CleanExiMM_JMJD3.
GenevisibleiQ5NCY0. MM.

Interactioni

Subunit structurei

Interacts with TLE1. Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B.By similarity

GO - Molecular functioni

  • beta-catenin binding Source: BHF-UCL

Protein-protein interaction databases

BioGridi229803. 5 interactors.
DIPiDIP-39160N.
IntActiQ5NCY0. 5 interactors.
STRINGi10090.ENSMUSP00000091620.

Structurei

Secondary structure

11641
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1160 – 1162Combined sources3
Beta strandi1170 – 1172Combined sources3
Helixi1176 – 1179Combined sources4
Beta strandi1185 – 1187Combined sources3
Helixi1191 – 1195Combined sources5
Helixi1197 – 1203Combined sources7
Beta strandi1209 – 1214Combined sources6
Helixi1216 – 1220Combined sources5
Helixi1224 – 1227Combined sources4
Helixi1229 – 1236Combined sources8
Beta strandi1240 – 1247Combined sources8
Beta strandi1260 – 1262Combined sources3
Beta strandi1269 – 1274Combined sources6
Helixi1275 – 1293Combined sources19
Beta strandi1323 – 1331Combined sources9
Turni1335 – 1338Combined sources4
Helixi1339 – 1344Combined sources6
Helixi1345 – 1347Combined sources3
Helixi1350 – 1352Combined sources3
Beta strandi1353 – 1355Combined sources3
Helixi1360 – 1363Combined sources4
Beta strandi1364 – 1366Combined sources3
Turni1369 – 1371Combined sources3
Beta strandi1375 – 1379Combined sources5
Beta strandi1384 – 1388Combined sources5
Helixi1391 – 1393Combined sources3
Beta strandi1395 – 1404Combined sources10
Beta strandi1406 – 1411Combined sources6
Helixi1413 – 1415Combined sources3
Helixi1416 – 1425Combined sources10
Turni1430 – 1432Combined sources3
Helixi1439 – 1444Combined sources6
Beta strandi1450 – 1454Combined sources5
Beta strandi1459 – 1462Combined sources4
Beta strandi1467 – 1483Combined sources17
Helixi1488 – 1503Combined sources16
Helixi1512 – 1522Combined sources11
Helixi1528 – 1553Combined sources26
Turni1554 – 1556Combined sources3
Beta strandi1559 – 1561Combined sources3
Turni1574 – 1576Combined sources3
Beta strandi1582 – 1588Combined sources7
Beta strandi1596 – 1599Combined sources4
Helixi1601 – 1607Combined sources7
Beta strandi1615 – 1620Combined sources6
Helixi1622 – 1631Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EYUX-ray2.30A/B1155-1293[»]
A/B1321-1641[»]
4EZ4X-ray2.99A/B1155-1293[»]
A/B1321-1641[»]
4EZHX-ray2.52A/B1155-1293[»]
A/B1321-1641[»]
ProteinModelPortaliQ5NCY0.
SMRiQ5NCY0.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1337 – 1500JmjCPROSITE-ProRule annotationAdd BLAST164

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi32 – 85Pro-richAdd BLAST54
Compositional biasi195 – 908Pro-richAdd BLAST714
Compositional biasi370 – 408Ser-richAdd BLAST39
Compositional biasi743 – 766Thr-richAdd BLAST24
Compositional biasi1045 – 1080Pro-richAdd BLAST36

Sequence similaritiesi

Belongs to the UTX family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG1124. Eukaryota.
KOG1246. Eukaryota.
ENOG410ZX0W. LUCA.
GeneTreeiENSGT00410000025758.
HOGENOMiHOG000113217.
InParanoidiQ5NCY0.
KOiK11448.
OMAiPLNKAPQ.
OrthoDBiEOG091G0OL6.
PhylomeDBiQ5NCY0.
TreeFamiTF317405.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR029518. KDM6B.
IPR011990. TPR-like_helical_dom.
[Graphical view]
PANTHERiPTHR14017:SF5. PTHR14017:SF5. 3 hits.
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q5NCY0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MHRAVDPPGA RSAREAFALG GLSCAGAWSS CPPHPPPRSS WLPGGRCSAS
60 70 80 90 100
VGQPPLSAPL PPSHGSSSGH PNKPYYAPGT PTPRPLHGKL ESLHGCVQAL
110 120 130 140 150
LREPAQPGLW EQLGQLYESE HDSEEAVCCY HRALRYGGSF AELGPRIGRL
160 170 180 190 200
QQAQLWNFHA GSCQHRAKVL PPLEQVWNLL HLEHKRNYGA KRGGPPVKRS
210 220 230 240 250
AEPPVVQPMP PAALSGPSGE EGLSPGGKRR RGCSSEQAGL PPGLPLPPPP
260 270 280 290 300
PPPPPPPPPP PPPPPPLPGL AISPPFQLTK PGLWNTLHGD AWGPERKGSA
310 320 330 340 350
PPERQEQRHS MPHSYPYPAP AYSAHPPSHR LVPNTPLGPG PRPPGAESHG
360 370 380 390 400
CLPATRPPGS DLRESRVQRS RMDSSVSPAA STACVPYAPS RPPGLPGTSS
410 420 430 440 450
SSSSSSSSNN TGLRGVEPSP GIPGADHYQN PALEISPHQA RLGPSAHSSR
460 470 480 490 500
KPFLTAPAAT PHLSLPPGTP SSPPPPCPRL LRPPPPPAWM KGSACRAARE
510 520 530 540 550
DGEILGELFF GAEGPPRPPP PPLPHRDGFL GPPNPRFSVG TQDSHNPPIP
560 570 580 590 600
PTTTSSSSSS NSHSSSPTGP VPFPPPSYLA RSIDPLPRPS SPTLSPQDPP
610 620 630 640 650
LPPLTLALPP APPSSCHQNT SGSFRRSESP RPRVSFPKTP EVGQGPPPGP
660 670 680 690 700
VSKAPQPVPP GVGELPARGP RLFDFPPTPL EDQFEEPAEF KILPDGLANI
710 720 730 740 750
MKMLDESIRK EEEQQQQQEA GVAPPPPLKE PFASLQPPFP SDTAPATTTA
760 770 780 790 800
APTTATTTTT TTTTTTQEEE KKPPPALPPP PPLAKFPPPP QPQPPPPPPA
810 820 830 840 850
SPASLLKSLA SVLEGQKYCY RGTGAAVSTR PGSVPATQYS PSPASGATAP
860 870 880 890 900
PPTSVAPSAQ GSPKPSVSSS SQFSTSGGPW AREHRAGEEP APGPVTPAQL
910 920 930 940 950
PPPLPLPPAR SESEVLEEIS RACETLVERV GRSAINPVDT ADPVDSGTEP
960 970 980 990 1000
QPPPAQAKEE SGGVAVAAAG PGSGKRRQKE HRRHRRACRD SVGRRPREGR
1010 1020 1030 1040 1050
AKAKAKAPKE KSRRVLGNLD LQSEEIQGRE KARPDVGGVS KVKTPTAPAP
1060 1070 1080 1090 1100
PPAPAPAAQP TPPSAPVPGK KTREEAPGPP GVSRADMLKL RSLSEGPPKE
1110 1120 1130 1140 1150
LKIRLIKVES GDKETFIASE VEERRLRMAD LTISHCAADV MRASKNAKVK
1160 1170 1180 1190 1200
GKFRESYLSP AQSVKPKINT EEKLPREKLN PPTPSIYLES KRDAFSPVLL
1210 1220 1230 1240 1250
QFCTDPRNPI TVIRGLAGSL RLNLGLFSTK TLVEASGEHT VEVRTQVQQP
1260 1270 1280 1290 1300
SDENWDLTGT RQIWPCESSR SHTTIAKYAQ YQASSFQESL QEERESEDEE
1310 1320 1330 1340 1350
SEEPDSTTGT SPSSAPDPKN HHIIKFGTNI DLSDAKRWKP QLQELLKLPA
1360 1370 1380 1390 1400
FMRVTSTGNM LSHVGHTILG MNTVQLYMKV PGSRTPGHQE NNNFCSVNIN
1410 1420 1430 1440 1450
IGPGDCEWFA VHEHYWETIS AFCDRHGVDY LTGSWWPILD DLYASNIPVY
1460 1470 1480 1490 1500
RFVQRPGDLV WINAGTVHWV QATGWCNNIA WNVGPLTAYQ YQLALERYEW
1510 1520 1530 1540 1550
NEVKNVKSIV PMIHVSWNVA RTVKISDPDL FKMIKFCLLQ SMKHCQVQRE
1560 1570 1580 1590 1600
SLVRAGKKIA YQGRVKDEPA YYCNECDVEV FNILFVTSEN GSRNTYLVHC
1610 1620 1630 1640
EGCARRRSAG LQGVVVLEQY RTEELAQAYD AFTLAPASTS R
Length:1,641
Mass (Da):176,355
Last modified:February 1, 2005 - v1
Checksum:i6CBE3620998427EA
GO

Sequence cautioni

The sequence BAE22775 differs from that shown. Reason: Erroneous initiation.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti172P → S in AAH75632 (PubMed:15489334).Curated1
Sequence conflicti965A → T in BAC97931 (PubMed:14621295).Curated1
Sequence conflicti1290L → LQ in BAC97931 (PubMed:14621295).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL596125 Genomic DNA. Translation: CAI35996.1.
BC075632 mRNA. Translation: AAH75632.1.
AK129121 mRNA. Translation: BAC97931.1.
AK136019 mRNA. Translation: BAE22775.1. Different initiation.
CCDSiCCDS24895.1.
RefSeqiNP_001017426.1. NM_001017426.1.
XP_006532961.1. XM_006532898.1.
XP_011247221.1. XM_011248919.2.
XP_011247222.1. XM_011248920.2.
XP_011247223.1. XM_011248921.1.
XP_011247224.1. XM_011248922.2.
XP_011247225.1. XM_011248923.1.
UniGeneiMm.261201.
Mm.472522.

Genome annotation databases

EnsembliENSMUST00000094077; ENSMUSP00000091620; ENSMUSG00000018476.
GeneIDi216850.
KEGGimmu:216850.
UCSCiuc007jqd.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL596125 Genomic DNA. Translation: CAI35996.1.
BC075632 mRNA. Translation: AAH75632.1.
AK129121 mRNA. Translation: BAC97931.1.
AK136019 mRNA. Translation: BAE22775.1. Different initiation.
CCDSiCCDS24895.1.
RefSeqiNP_001017426.1. NM_001017426.1.
XP_006532961.1. XM_006532898.1.
XP_011247221.1. XM_011248919.2.
XP_011247222.1. XM_011248920.2.
XP_011247223.1. XM_011248921.1.
XP_011247224.1. XM_011248922.2.
XP_011247225.1. XM_011248923.1.
UniGeneiMm.261201.
Mm.472522.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4EYUX-ray2.30A/B1155-1293[»]
A/B1321-1641[»]
4EZ4X-ray2.99A/B1155-1293[»]
A/B1321-1641[»]
4EZHX-ray2.52A/B1155-1293[»]
A/B1321-1641[»]
ProteinModelPortaliQ5NCY0.
SMRiQ5NCY0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi229803. 5 interactors.
DIPiDIP-39160N.
IntActiQ5NCY0. 5 interactors.
STRINGi10090.ENSMUSP00000091620.

PTM databases

iPTMnetiQ5NCY0.
PhosphoSitePlusiQ5NCY0.

Proteomic databases

MaxQBiQ5NCY0.
PaxDbiQ5NCY0.
PeptideAtlasiQ5NCY0.
PRIDEiQ5NCY0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000094077; ENSMUSP00000091620; ENSMUSG00000018476.
GeneIDi216850.
KEGGimmu:216850.
UCSCiuc007jqd.1. mouse.

Organism-specific databases

CTDi23135.
MGIiMGI:2448492. Kdm6b.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1124. Eukaryota.
KOG1246. Eukaryota.
ENOG410ZX0W. LUCA.
GeneTreeiENSGT00410000025758.
HOGENOMiHOG000113217.
InParanoidiQ5NCY0.
KOiK11448.
OMAiPLNKAPQ.
OrthoDBiEOG091G0OL6.
PhylomeDBiQ5NCY0.
TreeFamiTF317405.

Enzyme and pathway databases

ReactomeiR-MMU-2559580. Oxidative Stress Induced Senescence.
R-MMU-3214842. HDMs demethylate histones.

Miscellaneous databases

ChiTaRSiKdm6b. mouse.
PROiQ5NCY0.
SOURCEiSearch...

Gene expression databases

BgeeiENSMUSG00000018476.
CleanExiMM_JMJD3.
GenevisibleiQ5NCY0. MM.

Family and domain databases

Gene3Di1.25.40.10. 1 hit.
InterProiIPR003347. JmjC_dom.
IPR029518. KDM6B.
IPR011990. TPR-like_helical_dom.
[Graphical view]
PANTHERiPTHR14017:SF5. PTHR14017:SF5. 3 hits.
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM6B_MOUSE
AccessioniPrimary (citable) accession number: Q5NCY0
Secondary accession number(s): Q3UWY9, Q4VC26, Q6ZQD3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: February 1, 2005
Last modified: November 2, 2016
This is version 91 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.