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O15054 (KDM6B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | 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 6B

EC=1.14.11.-
Alternative name(s):
JmjC domain-containing protein 3
Jumonji domain-containing protein 3
Lysine demethylase 6B
Gene names
Name:KDM6B
Synonyms:JMJD3, KIAA0346
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1643 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.7

Cofactor

Ascorbate By similarity. Ref.6

Fe2+. Ref.6

Subunit structure

Interacts with TLE1 By similarity. Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B. Ref.6

Subcellular location

Nucleus Probable Ref.6.

Induction

By 12-O-tetradecanoylphorbol-13-acetate (TPA) in myeloid leukemia cells. Ref.5

Sequence similarities

Belongs to the UTX family.

Contains 1 JmjC domain.

Sequence caution

The sequence BAA21572.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

ESR1P033722EBI-2831260,EBI-78473

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 2 (identifier: O15054-2)

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.
Note: Gene prediction based on similarity to mouse ortholog.
Isoform 1 (identifier: O15054-1)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 16431643Lysine-specific demethylase 6B
PRO_0000292007

Regions

Domain1339 – 1502164JmjC
Compositional bias32 – 8554Pro-rich
Compositional bias195 – 906712Pro-rich
Compositional bias738 – 76427Thr-rich
Compositional bias1046 – 108237Pro-rich

Sites

Metal binding13901Iron Probable
Metal binding13921Iron Probable

Natural variations

Alternative sequence16361L → LVRARRARGQRRRALGQAAG TGFGSPAAPFPEPPPAFSPQ in isoform 1.
VSP_040102
Natural variant2031P → A.
Corresponds to variant rs60738318 [ dbSNP | Ensembl ].
VAR_061670
Natural variant3081S → L.
Corresponds to variant rs2270516 [ dbSNP | Ensembl ].
VAR_032927

Experimental info

Sequence conflict252 – 2543Missing in BAA21572. Ref.1
Sequence conflict252 – 2543Missing in AAH09994. Ref.3

Secondary structure

................................................................................. 1643
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 2 [UniParc].

Last modified November 30, 2010. Version 4.
Checksum: 8CE32AE602683BA3

FASTA1,643176,632
        10         20         30         40         50         60 
MHRAVDPPGA RAAREAFALG GLSCAGAWSS CPPHPPPRSA WLPGGRCSAS IGQPPLPAPL 

        70         80         90        100        110        120 
PPSHGSSSGH PSKPYYAPGA PTPRPLHGKL ESLHGCVQAL LREPAQPGLW EQLGQLYESE 

       130        140        150        160        170        180 
HDSEEATRCY HSALRYGGSF AELGPRIGRL QQAQLWNFHT GSCQHRAKVL PPLEQVWNLL 

       190        200        210        220        230        240 
HLEHKRNYGA KRGGPPVKRA AEPPVVQPVP PAALSGPSGE EGLSPGGKRR RGCNSEQTGL 

       250        260        270        280        290        300 
PPGLPLPPPP LPPPPPPPPP PPPPLPGLAT SPPFQLTKPG LWSTLHGDAW GPERKGSAPP 

       310        320        330        340        350        360 
ERQEQRHSLP HPYPYPAPAY TAHPPGHRLV PAAPPGPGPR PPGAESHGCL PATRPPGSDL 

       370        380        390        400        410        420 
RESRVQRSRM DSSVSPAATT ACVPYAPSRP PGLPGTTTSS SSSSSSNTGL RGVEPNPGIP 

       430        440        450        460        470        480 
GADHYQTPAL EVSHHGRLGP SAHSSRKPFL GAPAATPHLS LPPGPSSPPP PPCPRLLRPP 

       490        500        510        520        530        540 
PPPAWLKGPA CRAAREDGEI LEELFFGTEG PPRPAPPPLP HREGFLGPPA SRFSVGTQDS 

       550        560        570        580        590        600 
HTPPTPPTPT TSSSNSNSGS HSSSPAGPVS FPPPPYLARS IDPLPRPPSP AQNPQDPPLV 

       610        620        630        640        650        660 
PLTLALPPAP PSSCHQNTSG SFRRPESPRP RVSFPKTPEV GPGPPPGPLS KAPQPVPPGV 

       670        680        690        700        710        720 
GELPARGPRL FDFPPTPLED QFEEPAEFKI LPDGLANIMK MLDESIRKEE EQQQHEAGVA 

       730        740        750        760        770        780 
PQPPLKEPFA SLQSPFPTDT APTTTAPAVA VTTTTTTTTT TTATQEEEKK PPPALPPPPP 

       790        800        810        820        830        840 
LAKFPPPSQP QPPPPPPPSP ASLLKSLASV LEGQKYCYRG TGAAVSTRPG PLPTTQYSPG 

       850        860        870        880        890        900 
PPSGATALPP TSAAPSAQGS PQPSASSSSQ FSTSGGPWAR ERRAGEEPVP GPMTPTQPPP 

       910        920        930        940        950        960 
PLSLPPARSE SEVLEEISRA CETLVERVGR SATDPADPVD TAEPADSGTE RLLPPAQAKE 

       970        980        990       1000       1010       1020 
EAGGVAAVSG SCKRRQKEHQ KEHRRHRRAC KDSVGRRPRE GRAKAKAKVP KEKSRRVLGN 

      1030       1040       1050       1060       1070       1080 
LDLQSEEIQG REKSRPDLGG ASKAKPPTAP APPSAPAPSA QPTPPSASVP GKKAREEAPG 

      1090       1100       1110       1120       1130       1140 
PPGVSRADML KLRSLSEGPP KELKIRLIKV ESGDKETFIA SEVEERRLRM ADLTISHCAA 

      1150       1160       1170       1180       1190       1200 
DVVRASRNAK VKGKFRESYL SPAQSVKPKI NTEEKLPREK LNPPTPSIYL ESKRDAFSPV 

      1210       1220       1230       1240       1250       1260 
LLQFCTDPRN PITVIRGLAG SLRLNLGLFS TKTLVEASGE HTVEVRTQVQ QPSDENWDLT 

      1270       1280       1290       1300       1310       1320 
GTRQIWPCES SRSHTTIAKY AQYQASSFQE SLQEEKESED EESEEPDSTT GTPPSSAPDP 

      1330       1340       1350       1360       1370       1380 
KNHHIIKFGT NIDLSDAKRW KPQLQELLKL PAFMRVTSTG NMLSHVGHTI LGMNTVQLYM 

      1390       1400       1410       1420       1430       1440 
KVPGSRTPGH QENNNFCSVN INIGPGDCEW FAVHEHYWET ISAFCDRHGV DYLTGSWWPI 

      1450       1460       1470       1480       1490       1500 
LDDLYASNIP VYRFVQRPGD LVWINAGTVH WVQATGWCNN IAWNVGPLTA YQYQLALERY 

      1510       1520       1530       1540       1550       1560 
EWNEVKNVKS IVPMIHVSWN VARTVKISDP DLFKMIKFCL LQSMKHCQVQ RESLVRAGKK 

      1570       1580       1590       1600       1610       1620 
IAYQGRVKDE PAYYCNECDV EVFNILFVTS ENGSRNTYLV HCEGCARRRS AGLQGVVVLE 

      1630       1640 
QYRTEELAQA YDAFTLAPAS TSR 

« Hide

Isoform 1 [UniParc].

Checksum: E4264890580649AB
Show »

FASTA1,682180,702

References

« Hide 'large scale' references
[1]"Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro."
Nagase T., Ishikawa K., Nakajima D., Ohira M., Seki N., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 4:141-150(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Brain.
[2]"Construction of expression-ready cDNA clones for KIAA genes: manual curation of 330 KIAA cDNA clones."
Nakajima D., Okazaki N., Yamakawa H., Kikuno R., Ohara O., Nagase T.
DNA Res. 9:99-106(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SEQUENCE REVISION.
[3]"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage."
Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. expand/collapse author list , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C.
Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"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] OF 1000-1643 (ISOFORM 2).
Tissue: Brain.
[5]"An efficient strategy to identify early TPA-responsive genes during differentiation of HL-60 cells."
Hu L.Y., Tepper C.G., Lo S.H., Lin W.C.
Gene Expr. 13:179-189(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION BY TPA.
[6]"The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing."
De Santa F., Totaro M.G., Prosperini E., Notarbartolo S., Testa G., Natoli G.
Cell 130:1083-1094(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY, COFACTOR, SUBCELLULAR LOCATION, IDENTIFICATION IN THE MLL4 COMPLEX.
[7]"A histone H3 lysine 27 demethylase regulates animal posterior development."
Lan F., Bayliss P.E., Rinn J.L., Whetstine J.R., Wang J.K., Chen S., Iwase S., Alpatov R., Issaeva I., Canaani E., Roberts T.M., Chang H.Y., Shi Y.
Nature 449:689-694(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY.
[8]"Identification of JmjC domain-containing UTX and JMJD3 as histone H3 lysine 27 demethylases."
Hong S., Cho Y.W., Yu L.-R., Yu H., Veenstra T.D., Ge K.
Proc. Natl. Acad. Sci. U.S.A. 104:18439-18444(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME ACTIVITY.
[9]"Crystal structure of the human JMJD3 Jumonji domain."
Structural genomics consortium (SGC)
Submitted (DEC-2010) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 1176-1502 IN COMPLEX WITH NICKEL IONS AND 8-HYDROXYQUINOLINE-5-CARBOXYLIC ACID.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB002344 mRNA. Translation: BAA21572.2. Different initiation.
AC104581 Genomic DNA. No translation available.
BC009994 mRNA. Translation: AAH09994.1.
CCDSCCDS32552.1. [O15054-1]
RefSeqNP_001073893.1. NM_001080424.1. [O15054-1]
XP_005256606.1. XM_005256549.1. [O15054-1]
XP_005256607.1. XM_005256550.2. [O15054-1]
XP_005256608.1. XM_005256551.1. [O15054-1]
XP_005256609.1. XM_005256552.2. [O15054-1]
XP_005256611.1. XM_005256554.2. [O15054-2]
XP_006721546.1. XM_006721483.1. [O15054-1]
UniGeneHs.223678.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2XUEX-ray2.00A/B1141-1643[»]
2XXZX-ray1.80A/B1176-1505[»]
4ASKX-ray1.86A/B1141-1643[»]
ProteinModelPortalO15054.
SMRO15054. Positions 1157-1638.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116752. 12 interactions.
DIPDIP-59912N.
IntActO15054. 5 interactions.
MINTMINT-7002224.
STRING9606.ENSP00000254846.

Chemistry

BindingDBO15054.
ChEMBLCHEMBL1938211.
GuidetoPHARMACOLOGY2685.

PTM databases

PhosphoSiteO15054.

Proteomic databases

MaxQBO15054.
PaxDbO15054.
PRIDEO15054.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000254846; ENSP00000254846; ENSG00000132510. [O15054-1]
ENST00000448097; ENSP00000412513; ENSG00000132510. [O15054-2]
GeneID23135.
KEGGhsa:23135.
UCSCuc002giw.1. human. [O15054-1]
uc002gix.3. human. [O15054-2]

Organism-specific databases

CTD23135.
GeneCardsGC17P007686.
HGNCHGNC:29012. KDM6B.
HPAHPA037988.
MIM611577. gene.
neXtProtNX_O15054.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG246325.
HOGENOMHOG000113217.
InParanoidO15054.
KOK11448.
OMAMDPLPRP.
OrthoDBEOG7CG6Z5.
PhylomeDBO15054.
TreeFamTF317405.

Enzyme and pathway databases

ReactomeREACT_120956. Cellular responses to stress.

Gene expression databases

ArrayExpressO15054.
BgeeO15054.
CleanExHS_JMJD3.
GenevestigatorO15054.

Family and domain databases

InterProIPR003347. JmjC_dom.
[Graphical view]
PfamPF02373. JmjC. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO15054.
GenomeRNAi23135.
NextBio44391.
PROO15054.
SOURCESearch...

Entry information

Entry nameKDM6B_HUMAN
AccessionPrimary (citable) accession number: O15054
Secondary accession number(s): C9IZ40, Q96G33
Entry history
Integrated into UniProtKB/Swiss-Prot: June 26, 2007
Last sequence update: November 30, 2010
Last modified: July 9, 2014
This is version 106 of the entry and version 4 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM