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Protein

Lysine-specific demethylase 6B

Gene

KDM6B

Organism
Homo sapiens (Human)
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.2 Publications

Cofactori

Protein has several cofactor binding sites:

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1390IronCurated1
Metal bindingi1392IronCurated1
Metal bindingi1470IronBy similarity1
Metal bindingi1575ZincBy similarity1
Metal bindingi1578ZincBy similarity1
Metal bindingi1602ZincBy similarity1
Metal bindingi1605ZincBy similarity1

GO - Molecular functioni

GO - Biological processi

  • cardiac muscle cell differentiation Source: BHF-UCL
  • cell fate commitment Source: Ensembl
  • cellular response to hydrogen peroxide Source: Ensembl
  • endothelial cell differentiation Source: BHF-UCL
  • hippocampus development Source: Ensembl
  • 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
  • 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

BioCyciZFISH:ENSG00000132510-MONOMER.
ReactomeiR-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-3214842. HDMs demethylate histones.
SIGNORiO15054.

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
Lysine demethylase 6B
Gene namesi
Name:KDM6B
Synonyms:JMJD3, KIAA0346
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 17

Organism-specific databases

HGNCiHGNC:29012. KDM6B.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

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

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi23135.
OpenTargetsiENSG00000132510.

Chemistry databases

ChEMBLiCHEMBL1938211.
GuidetoPHARMACOLOGYi2685.

Polymorphism and mutation databases

BioMutaiKDM6B.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002920071 – 1643Lysine-specific demethylase 6BAdd BLAST1643

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei224PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiO15054.
PeptideAtlasiO15054.
PRIDEiO15054.

PTM databases

iPTMnetiO15054.
PhosphoSitePlusiO15054.

Expressioni

Inductioni

By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells.1 Publication

Gene expression databases

BgeeiENSG00000132510.
CleanExiHS_JMJD3.
ExpressionAtlasiO15054. baseline and differential.
GenevisibleiO15054. HS.

Organism-specific databases

HPAiHPA037988.

Interactioni

Subunit structurei

Interacts with TLE1 (By similarity). Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B.By similarity2 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
ESR1P033722EBI-2831260,EBI-78473

Protein-protein interaction databases

BioGridi116752. 12 interactors.
DIPiDIP-59912N.
IntActiO15054. 6 interactors.
MINTiMINT-7002224.
STRINGi9606.ENSP00000254846.

Chemistry databases

BindingDBiO15054.

Structurei

Secondary structure

11643
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi1178 – 1181Combined sources4
Beta strandi1187 – 1189Combined sources3
Helixi1193 – 1195Combined sources3
Helixi1199 – 1206Combined sources8
Beta strandi1211 – 1217Combined sources7
Helixi1218 – 1222Combined sources5
Helixi1226 – 1229Combined sources4
Helixi1231 – 1238Combined sources8
Beta strandi1242 – 1249Combined sources8
Beta strandi1261 – 1264Combined sources4
Beta strandi1271 – 1276Combined sources6
Helixi1277 – 1289Combined sources13
Beta strandi1325 – 1333Combined sources9
Helixi1337 – 1347Combined sources11
Helixi1352 – 1354Combined sources3
Turni1356 – 1359Combined sources4
Beta strandi1363 – 1365Combined sources3
Beta strandi1366 – 1368Combined sources3
Turni1371 – 1373Combined sources3
Beta strandi1375 – 1381Combined sources7
Beta strandi1386 – 1390Combined sources5
Helixi1393 – 1395Combined sources3
Beta strandi1397 – 1406Combined sources10
Beta strandi1408 – 1413Combined sources6
Helixi1415 – 1417Combined sources3
Helixi1418 – 1427Combined sources10
Turni1432 – 1434Combined sources3
Helixi1441 – 1446Combined sources6
Beta strandi1452 – 1456Combined sources5
Beta strandi1461 – 1464Combined sources4
Beta strandi1469 – 1487Combined sources19
Helixi1491 – 1495Combined sources5
Helixi1497 – 1501Combined sources5
Helixi1514 – 1524Combined sources11
Helixi1530 – 1557Combined sources28
Beta strandi1561 – 1563Combined sources3
Turni1576 – 1578Combined sources3
Beta strandi1584 – 1590Combined sources7
Beta strandi1592 – 1596Combined sources5
Beta strandi1598 – 1601Combined sources4
Helixi1603 – 1608Combined sources6
Turni1610 – 1615Combined sources6
Beta strandi1617 – 1622Combined sources6
Helixi1624 – 1633Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XUEX-ray2.00A/B1141-1643[»]
2XXZX-ray1.80A/B1176-1505[»]
4ASKX-ray1.86A/B1141-1643[»]
5FP3X-ray2.05A/B1141-1643[»]
ProteinModelPortaliO15054.
SMRiO15054.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO15054.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1339 – 1502JmjCPROSITE-ProRule annotationAdd BLAST164

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi32 – 85Pro-richAdd BLAST54
Compositional biasi195 – 906Pro-richAdd BLAST712
Compositional biasi738 – 764Thr-richAdd BLAST27
Compositional biasi1046 – 1082Pro-richAdd BLAST37

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiKOG1124. Eukaryota.
KOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00410000025758.
HOGENOMiHOG000113217.
InParanoidiO15054.
KOiK11448.
OMAiPLNKAPQ.
OrthoDBiEOG091G0OL6.
PhylomeDBiO15054.
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]

Sequences (2)i

Sequence statusi: Complete.

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

Isoform 2 (identifier: O15054-2) [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
MHRAVDPPGA RAAREAFALG GLSCAGAWSS CPPHPPPRSA WLPGGRCSAS
60 70 80 90 100
IGQPPLPAPL PPSHGSSSGH PSKPYYAPGA PTPRPLHGKL ESLHGCVQAL
110 120 130 140 150
LREPAQPGLW EQLGQLYESE HDSEEATRCY HSALRYGGSF AELGPRIGRL
160 170 180 190 200
QQAQLWNFHT GSCQHRAKVL PPLEQVWNLL HLEHKRNYGA KRGGPPVKRA
210 220 230 240 250
AEPPVVQPVP PAALSGPSGE EGLSPGGKRR RGCNSEQTGL PPGLPLPPPP
260 270 280 290 300
LPPPPPPPPP PPPPLPGLAT SPPFQLTKPG LWSTLHGDAW GPERKGSAPP
310 320 330 340 350
ERQEQRHSLP HPYPYPAPAY TAHPPGHRLV PAAPPGPGPR PPGAESHGCL
360 370 380 390 400
PATRPPGSDL RESRVQRSRM DSSVSPAATT ACVPYAPSRP PGLPGTTTSS
410 420 430 440 450
SSSSSSNTGL RGVEPNPGIP GADHYQTPAL EVSHHGRLGP SAHSSRKPFL
460 470 480 490 500
GAPAATPHLS LPPGPSSPPP PPCPRLLRPP PPPAWLKGPA CRAAREDGEI
510 520 530 540 550
LEELFFGTEG PPRPAPPPLP HREGFLGPPA SRFSVGTQDS HTPPTPPTPT
560 570 580 590 600
TSSSNSNSGS HSSSPAGPVS FPPPPYLARS IDPLPRPPSP AQNPQDPPLV
610 620 630 640 650
PLTLALPPAP PSSCHQNTSG SFRRPESPRP RVSFPKTPEV GPGPPPGPLS
660 670 680 690 700
KAPQPVPPGV GELPARGPRL FDFPPTPLED QFEEPAEFKI LPDGLANIMK
710 720 730 740 750
MLDESIRKEE EQQQHEAGVA PQPPLKEPFA SLQSPFPTDT APTTTAPAVA
760 770 780 790 800
VTTTTTTTTT TTATQEEEKK PPPALPPPPP LAKFPPPSQP QPPPPPPPSP
810 820 830 840 850
ASLLKSLASV LEGQKYCYRG TGAAVSTRPG PLPTTQYSPG PPSGATALPP
860 870 880 890 900
TSAAPSAQGS PQPSASSSSQ FSTSGGPWAR ERRAGEEPVP GPMTPTQPPP
910 920 930 940 950
PLSLPPARSE SEVLEEISRA CETLVERVGR SATDPADPVD TAEPADSGTE
960 970 980 990 1000
RLLPPAQAKE EAGGVAAVSG SCKRRQKEHQ KEHRRHRRAC KDSVGRRPRE
1010 1020 1030 1040 1050
GRAKAKAKVP KEKSRRVLGN LDLQSEEIQG REKSRPDLGG ASKAKPPTAP
1060 1070 1080 1090 1100
APPSAPAPSA QPTPPSASVP GKKAREEAPG PPGVSRADML KLRSLSEGPP
1110 1120 1130 1140 1150
KELKIRLIKV ESGDKETFIA SEVEERRLRM ADLTISHCAA DVVRASRNAK
1160 1170 1180 1190 1200
VKGKFRESYL SPAQSVKPKI NTEEKLPREK LNPPTPSIYL ESKRDAFSPV
1210 1220 1230 1240 1250
LLQFCTDPRN PITVIRGLAG SLRLNLGLFS TKTLVEASGE HTVEVRTQVQ
1260 1270 1280 1290 1300
QPSDENWDLT GTRQIWPCES SRSHTTIAKY AQYQASSFQE SLQEEKESED
1310 1320 1330 1340 1350
EESEEPDSTT GTPPSSAPDP KNHHIIKFGT NIDLSDAKRW KPQLQELLKL
1360 1370 1380 1390 1400
PAFMRVTSTG NMLSHVGHTI LGMNTVQLYM KVPGSRTPGH QENNNFCSVN
1410 1420 1430 1440 1450
INIGPGDCEW FAVHEHYWET ISAFCDRHGV DYLTGSWWPI LDDLYASNIP
1460 1470 1480 1490 1500
VYRFVQRPGD LVWINAGTVH WVQATGWCNN IAWNVGPLTA YQYQLALERY
1510 1520 1530 1540 1550
EWNEVKNVKS IVPMIHVSWN VARTVKISDP DLFKMIKFCL LQSMKHCQVQ
1560 1570 1580 1590 1600
RESLVRAGKK IAYQGRVKDE PAYYCNECDV EVFNILFVTS ENGSRNTYLV
1610 1620 1630 1640
HCEGCARRRS AGLQGVVVLE QYRTEELAQA YDAFTLAPAS TSR
Note: Gene prediction based on similarity to mouse ortholog.
Length:1,643
Mass (Da):176,632
Last modified:November 30, 2010 - v4
Checksum:i8CE32AE602683BA3
GO
Isoform 1 (identifier: O15054-1) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1636-1636: L → LVRARRARGQRRRALGQAAGTGFGSPAAPFPEPPPAFSPQ

Show »
Length:1,682
Mass (Da):180,702
Checksum:iE4264890580649AB
GO

Sequence cautioni

The sequence BAA21572 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti252 – 254Missing in BAA21572 (PubMed:9205841).Curated3
Sequence conflicti252 – 254Missing in AAH09994 (PubMed:16625196).Curated3

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_061670203P → A.Corresponds to variant rs60738318dbSNPEnsembl.1
Natural variantiVAR_032927308S → L.Corresponds to variant rs2270516dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0401021636L → LVRARRARGQRRRALGQAAG TGFGSPAAPFPEPPPAFSPQ in isoform 1. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002344 mRNA. Translation: BAA21572.2. Different initiation.
AC104581 Genomic DNA. No translation available.
BC009994 mRNA. Translation: AAH09994.1.
CCDSiCCDS32552.1. [O15054-1]
RefSeqiNP_001073893.1. NM_001080424.1. [O15054-1]
XP_005256606.1. XM_005256549.3. [O15054-1]
XP_005256607.1. XM_005256550.4. [O15054-1]
XP_005256608.1. XM_005256551.3. [O15054-1]
XP_005256609.1. XM_005256552.4. [O15054-1]
XP_006721546.1. XM_006721483.3. [O15054-1]
XP_011522052.1. XM_011523750.2. [O15054-1]
XP_011522054.1. XM_011523752.2. [O15054-1]
XP_016879870.1. XM_017024381.1. [O15054-2]
UniGeneiHs.223678.

Genome annotation databases

EnsembliENST00000254846; ENSP00000254846; ENSG00000132510. [O15054-1]
ENST00000448097; ENSP00000412513; ENSG00000132510. [O15054-2]
GeneIDi23135.
KEGGihsa:23135.
UCSCiuc002giw.2. human. [O15054-2]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002344 mRNA. Translation: BAA21572.2. Different initiation.
AC104581 Genomic DNA. No translation available.
BC009994 mRNA. Translation: AAH09994.1.
CCDSiCCDS32552.1. [O15054-1]
RefSeqiNP_001073893.1. NM_001080424.1. [O15054-1]
XP_005256606.1. XM_005256549.3. [O15054-1]
XP_005256607.1. XM_005256550.4. [O15054-1]
XP_005256608.1. XM_005256551.3. [O15054-1]
XP_005256609.1. XM_005256552.4. [O15054-1]
XP_006721546.1. XM_006721483.3. [O15054-1]
XP_011522052.1. XM_011523750.2. [O15054-1]
XP_011522054.1. XM_011523752.2. [O15054-1]
XP_016879870.1. XM_017024381.1. [O15054-2]
UniGeneiHs.223678.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2XUEX-ray2.00A/B1141-1643[»]
2XXZX-ray1.80A/B1176-1505[»]
4ASKX-ray1.86A/B1141-1643[»]
5FP3X-ray2.05A/B1141-1643[»]
ProteinModelPortaliO15054.
SMRiO15054.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi116752. 12 interactors.
DIPiDIP-59912N.
IntActiO15054. 6 interactors.
MINTiMINT-7002224.
STRINGi9606.ENSP00000254846.

Chemistry databases

BindingDBiO15054.
ChEMBLiCHEMBL1938211.
GuidetoPHARMACOLOGYi2685.

PTM databases

iPTMnetiO15054.
PhosphoSitePlusiO15054.

Polymorphism and mutation databases

BioMutaiKDM6B.

Proteomic databases

PaxDbiO15054.
PeptideAtlasiO15054.
PRIDEiO15054.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000254846; ENSP00000254846; ENSG00000132510. [O15054-1]
ENST00000448097; ENSP00000412513; ENSG00000132510. [O15054-2]
GeneIDi23135.
KEGGihsa:23135.
UCSCiuc002giw.2. human. [O15054-2]

Organism-specific databases

CTDi23135.
DisGeNETi23135.
GeneCardsiKDM6B.
HGNCiHGNC:29012. KDM6B.
HPAiHPA037988.
MIMi611577. gene.
neXtProtiNX_O15054.
OpenTargetsiENSG00000132510.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1124. Eukaryota.
KOG1246. Eukaryota.
ENOG410XR9J. LUCA.
GeneTreeiENSGT00410000025758.
HOGENOMiHOG000113217.
InParanoidiO15054.
KOiK11448.
OMAiPLNKAPQ.
OrthoDBiEOG091G0OL6.
PhylomeDBiO15054.
TreeFamiTF317405.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000132510-MONOMER.
ReactomeiR-HSA-2559580. Oxidative Stress Induced Senescence.
R-HSA-3214842. HDMs demethylate histones.
SIGNORiO15054.

Miscellaneous databases

ChiTaRSiKDM6B. human.
EvolutionaryTraceiO15054.
GenomeRNAii23135.
PROiO15054.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000132510.
CleanExiHS_JMJD3.
ExpressionAtlasiO15054. baseline and differential.
GenevisibleiO15054. HS.

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_HUMAN
AccessioniPrimary (citable) accession number: O15054
Secondary accession number(s): C9IZ40, Q96G33
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: November 30, 2010
Last modified: November 30, 2016
This is version 130 of the entry and version 4 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 17
    Human chromosome 17: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.