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Protein

Lysine-specific demethylase 3B

Gene

KDM3B

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-9' of histone H3, thereby playing a central role in histone code. Demethylation of Lys residue generates formaldehyde and succinate. May have tumor suppressor activity.1 Publication

Cofactori

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

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi1560Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi1562Iron; catalyticPROSITE-ProRule annotation1
Metal bindingi1689Iron; catalyticPROSITE-ProRule annotation1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1031 – 1056C6-typeSequence analysisAdd BLAST26

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
Recommended name:
Lysine-specific demethylase 3B (EC:1.14.11.-)
Alternative name(s):
JmjC domain-containing histone demethylation protein 2B
Jumonji domain-containing protein 1B
Nuclear protein 5qNCA
Gene namesi
Name:KDM3B
Synonyms:C5orf7, JHDM2B, JMJD1B, KIAA1082
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

HGNCiHGNC:1337. KDM3B.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi51780.
OpenTargetsiENSG00000120733.
PharmGKBiPA25918.

Polymorphism and mutation databases

BioMutaiKDM3B.
DMDMi308153456.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemovedCombined sources
ChainiPRO_00002343732 – 1761Lysine-specific demethylase 3BAdd BLAST1760

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylalanineCombined sources1
Modified residuei361N6-acetyllysineCombined sources1
Modified residuei492PhosphoserineCombined sources1
Modified residuei546PhosphoserineBy similarity1
Modified residuei556PhosphoserineBy similarity1
Modified residuei560PhosphoserineCombined sources1
Modified residuei614PhosphothreonineCombined sources1
Modified residuei766PhosphoserineCombined sources1
Modified residuei773PhosphoserineCombined sources1
Modified residuei778PhosphoserineCombined sources1
Modified residuei779PhosphoserineCombined sources1
Modified residuei798PhosphoserineCombined sources1
Modified residuei1253PhosphoserineCombined sources1
Modified residuei1259PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ7LBC6.
MaxQBiQ7LBC6.
PaxDbiQ7LBC6.
PeptideAtlasiQ7LBC6.
PRIDEiQ7LBC6.

PTM databases

iPTMnetiQ7LBC6.
PhosphoSitePlusiQ7LBC6.

Expressioni

Tissue specificityi

Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver.2 Publications

Gene expression databases

BgeeiENSG00000120733.
CleanExiHS_JMJD1B.
ExpressionAtlasiQ7LBC6. baseline and differential.
GenevisibleiQ7LBC6. HS.

Organism-specific databases

HPAiHPA016610.
HPA057202.

Interactioni

Protein-protein interaction databases

BioGridi119727. 28 interactors.
IntActiQ7LBC6. 10 interactors.
MINTiMINT-1195273.
STRINGi9606.ENSP00000326563.

Structurei

Secondary structure

11761
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi1382 – 1385Combined sources4
Turni1386 – 1389Combined sources4
Beta strandi1390 – 1394Combined sources5
Helixi1401 – 1410Combined sources10
Beta strandi1415 – 1417Combined sources3
Helixi1420 – 1423Combined sources4
Helixi1426 – 1429Combined sources4
Helixi1431 – 1438Combined sources8
Beta strandi1441 – 1447Combined sources7
Turni1448 – 1450Combined sources3
Beta strandi1453 – 1458Combined sources6
Helixi1459 – 1464Combined sources6
Turni1465 – 1467Combined sources3
Helixi1469 – 1471Combined sources3
Beta strandi1483 – 1485Combined sources3
Helixi1493 – 1497Combined sources5
Helixi1499 – 1508Combined sources10
Helixi1512 – 1515Combined sources4
Turni1524 – 1526Combined sources3
Beta strandi1539 – 1543Combined sources5
Helixi1550 – 1553Combined sources4
Beta strandi1556 – 1560Combined sources5
Beta strandi1563 – 1574Combined sources12
Beta strandi1577 – 1579Combined sources3
Helixi1583 – 1592Combined sources10
Helixi1597 – 1604Combined sources8
Beta strandi1610 – 1616Combined sources7
Helixi1619 – 1621Combined sources3
Helixi1622 – 1634Combined sources13
Helixi1646 – 1649Combined sources4
Helixi1656 – 1666Combined sources11
Beta strandi1671 – 1676Combined sources6
Beta strandi1680 – 1683Combined sources4
Beta strandi1689 – 1704Combined sources16
Helixi1707 – 1709Combined sources3
Helixi1710 – 1719Combined sources10

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C8DX-ray2.18A1380-1720[»]
ProteinModelPortaliQ7LBC6.
SMRiQ7LBC6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini1498 – 1721JmjCPROSITE-ProRule annotationAdd BLAST224

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi1293 – 1297LXXLL motif5

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi647 – 744Ser-richAdd BLAST98

Domaini

Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the association with nuclear receptors.By similarity

Sequence similaritiesi

Belongs to the JHDM2 histone demethylase family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri1031 – 1056C6-typeSequence analysisAdd BLAST26

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
GeneTreeiENSGT00530000063039.
InParanoidiQ7LBC6.
KOiK15601.
OMAiIICKRLR.
OrthoDBiEOG091G00RB.
PhylomeDBiQ7LBC6.
TreeFamiTF324723.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q7LBC6-1) [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
MADAAASPVG KRLLLLFADT AASASASAPA AAAASGDPGP ALRTRAWRAG
60 70 80 90 100
TVRAMSGAVP QDLAIFVEFD GCNWKQHSWV KVHAEEVIVL LLEGSLVWAP
110 120 130 140 150
REDPVLLQGI RVSIAQWPAL TFTPLVDKLG LGSVVPVEYL LDRELRFLSD
160 170 180 190 200
ANGLHLFQMG TDSQNQILLE HAALRETVNA LISDQKLQEI FSRGPYSVQG
210 220 230 240 250
HRVKIYQPEG EEGWLYGVVS HQDSITRLME VSVTESGEIK SVDPRLIHVM
260 270 280 290 300
LMDNSAPQSE GGTLKAVKSS KGKKKRESIE GKDGRRRKSA SDSGCDPASK
310 320 330 340 350
KLKGDRGEVD SNGSDGGEAS RGPWKGGNAS GEPGLDQRAK QPPSTFVPQI
360 370 380 390 400
NRNIRFATYT KENGRTLVVQ DEPVGGDTPA SFTPYSTATG QTPLAPEVGG
410 420 430 440 450
AENKEAGKTL EQVGQGIVAS AAVVTTASST PNTVRISDTG LAAGTVPEKQ
460 470 480 490 500
KGSRSQASGE NSRNSILASS GFGAPLPSSS QPLTFGSGRS QSNGVLATEN
510 520 530 540 550
KPLGFSFGCS SAQEAQKDTD LSKNLFFQCM SQTLPTSNYF TTVSESLADD
560 570 580 590 600
SSSRDSFKQS LESLSSGLCK GRSVLGTDTK PGSKAGSSVD RKVPAESMPT
610 620 630 640 650
LTPAFPRSLL NARTPENHEN LFLQPPKLSR EEPSNPFLAF VEKVEHSPFS
660 670 680 690 700
SFASQASGSS SSATTVTSKV APSWPESHSS ADSASLAKKK PLFITTDSSK
710 720 730 740 750
LVSGVLGSAL TSGGPSLSAM GNGRSSSPTS SLTQPIEMPT LSSSPTEERP
760 770 780 790 800
TVGPGQQDNP LLKTFSNVFG RHSGGFLSSP ADFSQENKAP FEAVKRFSLD
810 820 830 840 850
ERSLACRQDS DSSTNSDLSD LSDSEEQLQA KTGLKGIPEH LMGKLGPNGE
860 870 880 890 900
RSAELLLGKS KGKQAPKGRP RTAPLKVGQS VLKDVSKVKK LKQSGEPFLQ
910 920 930 940 950
DGSCINVAPH LHKCRECRLE RYRKFKEQEQ DDSTVACRFF HFRRLIFTRK
960 970 980 990 1000
GVLRVEGFLS PQQSDPDAMN LWIPSSSLAE GIDLETSKYI LANVGDQFCQ
1010 1020 1030 1040 1050
LVMSEKEAMM MVEPHQKVAW KRAVRGVREM CDVCETTLFN IHWVCRKCGF
1060 1070 1080 1090 1100
GVCLDCYRLR KSRPRSETEE MGDEEVFSWL KCAKGQSHEP ENLMPTQIIP
1110 1120 1130 1140 1150
GTALYNIGDM VHAARGKWGI KANCPCISRQ NKSVLRPAVT NGMSQLPSIN
1160 1170 1180 1190 1200
PSASSGNETT FSGGGGPAPV TTPEPDHVPK ADSTDIRSEE PLKTDSSASN
1210 1220 1230 1240 1250
SNSELKAIRP PCPDTAPPSS ALHWLADLAT QKAKEETKEA GSLRSVLNKE
1260 1270 1280 1290 1300
SHSPFGLDSF NSTAKVSPLT PKLFNSLLLG PTASNNKTEG SSLRDLLHSG
1310 1320 1330 1340 1350
PGKLPQTPLD TGIPFPPVFS TSSAGVKSKA SLPNFLDHII ASVVENKKTS
1360 1370 1380 1390 1400
DASKRACNLT DTQKEVKEMV MGLNVLDPHT SHSWLCDGRL LCLHDPSNKN
1410 1420 1430 1440 1450
NWKIFRECWK QGQPVLVSGV HKKLKSELWK PEAFSQEFGD QDVDLVNCRN
1460 1470 1480 1490 1500
CAIISDVKVR DFWDGFEIIC KRLRSEDGQP MVLKLKDWPP GEDFRDMMPT
1510 1520 1530 1540 1550
RFEDLMENLP LPEYTKRDGR LNLASRLPSY FVRPDLGPKM YNAYGLITAE
1560 1570 1580 1590 1600
DRRVGTTNLH LDVSDAVNVM VYVGIPIGEG AHDEEVLKTI DEGDADEVTK
1610 1620 1630 1640 1650
QRIHDGKEKP GALWHIYAAK DAEKIRELLR KVGEEQGQEN PPDHDPIHDQ
1660 1670 1680 1690 1700
SWYLDQTLRK RLYEEYGVQG WAIVQFLGDA VFIPAGAPHQ VHNLYSCIKV
1710 1720 1730 1740 1750
AEDFVSPEHV KHCFRLTQEF RHLSNTHTNH EDKLQVKNII YHAVKDAVGT
1760
LKAHESKLAR S
Length:1,761
Mass (Da):191,581
Last modified:October 5, 2010 - v2
Checksum:iFB900FCBF0675CD8
GO
Isoform 2 (identifier: Q7LBC6-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-344: Missing.
     345-349: TFVPQ → MGAME

Show »
Length:1,417
Mass (Da):154,668
Checksum:iAF66C2E416D31F40
GO
Isoform 3 (identifier: Q7LBC6-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1002: Missing.

Note: No experimental confirmation available.
Show »
Length:759
Mass (Da):84,712
Checksum:i5A13F19C0EE952EF
GO

Sequence cautioni

The sequence BAA83034 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti569C → R in AAF63765 (PubMed:11087669).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_026221256A → T.4 PublicationsCorresponds to variant rs6865472dbSNPEnsembl.1
Natural variantiVAR_0262221201S → N.Corresponds to variant rs7706614dbSNPEnsembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0182981 – 1002Missing in isoform 3. 1 PublicationAdd BLAST1002
Alternative sequenceiVSP_0182991 – 344Missing in isoform 2. 1 PublicationAdd BLAST344
Alternative sequenceiVSP_018300345 – 349TFVPQ → MGAME in isoform 2. 1 Publication5

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF251039 mRNA. Translation: AAF63765.1.
AF338242 mRNA. Translation: AAK13499.1.
AB029005 mRNA. Translation: BAA83034.2. Different initiation.
AC104116 Genomic DNA. No translation available.
AC113403 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW62141.1.
BC000539 mRNA. Translation: AAH00539.2.
BC001202 mRNA. Translation: AAH01202.1.
BC146788 mRNA. Translation: AAI46789.1.
CCDSiCCDS34242.1. [Q7LBC6-1]
RefSeqiNP_057688.2. NM_016604.3.
UniGeneiHs.483486.

Genome annotation databases

EnsembliENST00000314358; ENSP00000326563; ENSG00000120733. [Q7LBC6-1]
ENST00000542866; ENSP00000439462; ENSG00000120733. [Q7LBC6-3]
GeneIDi51780.
KEGGihsa:51780.
UCSCiuc003lcy.1. human. [Q7LBC6-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF251039 mRNA. Translation: AAF63765.1.
AF338242 mRNA. Translation: AAK13499.1.
AB029005 mRNA. Translation: BAA83034.2. Different initiation.
AC104116 Genomic DNA. No translation available.
AC113403 Genomic DNA. No translation available.
CH471062 Genomic DNA. Translation: EAW62141.1.
BC000539 mRNA. Translation: AAH00539.2.
BC001202 mRNA. Translation: AAH01202.1.
BC146788 mRNA. Translation: AAI46789.1.
CCDSiCCDS34242.1. [Q7LBC6-1]
RefSeqiNP_057688.2. NM_016604.3.
UniGeneiHs.483486.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
4C8DX-ray2.18A1380-1720[»]
ProteinModelPortaliQ7LBC6.
SMRiQ7LBC6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119727. 28 interactors.
IntActiQ7LBC6. 10 interactors.
MINTiMINT-1195273.
STRINGi9606.ENSP00000326563.

PTM databases

iPTMnetiQ7LBC6.
PhosphoSitePlusiQ7LBC6.

Polymorphism and mutation databases

BioMutaiKDM3B.
DMDMi308153456.

Proteomic databases

EPDiQ7LBC6.
MaxQBiQ7LBC6.
PaxDbiQ7LBC6.
PeptideAtlasiQ7LBC6.
PRIDEiQ7LBC6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000314358; ENSP00000326563; ENSG00000120733. [Q7LBC6-1]
ENST00000542866; ENSP00000439462; ENSG00000120733. [Q7LBC6-3]
GeneIDi51780.
KEGGihsa:51780.
UCSCiuc003lcy.1. human. [Q7LBC6-1]

Organism-specific databases

CTDi51780.
DisGeNETi51780.
GeneCardsiKDM3B.
HGNCiHGNC:1337. KDM3B.
HPAiHPA016610.
HPA057202.
MIMi609373. gene.
neXtProtiNX_Q7LBC6.
OpenTargetsiENSG00000120733.
PharmGKBiPA25918.
HUGEiSearch...
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
GeneTreeiENSGT00530000063039.
InParanoidiQ7LBC6.
KOiK15601.
OMAiIICKRLR.
OrthoDBiEOG091G00RB.
PhylomeDBiQ7LBC6.
TreeFamiTF324723.

Enzyme and pathway databases

ReactomeiR-HSA-3214842. HDMs demethylate histones.

Miscellaneous databases

ChiTaRSiKDM3B. human.
GeneWikiiJMJD1B.
GenomeRNAii51780.
PROiQ7LBC6.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000120733.
CleanExiHS_JMJD1B.
ExpressionAtlasiQ7LBC6. baseline and differential.
GenevisibleiQ7LBC6. HS.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiKDM3B_HUMAN
AccessioniPrimary (citable) accession number: Q7LBC6
Secondary accession number(s): A6H8X7
, Q9BVH6, Q9BW93, Q9BZ52, Q9NYF4, Q9UPS0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: October 5, 2010
Last modified: November 30, 2016
This is version 114 of the entry and version 2 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

Miscellaneous

Its gene is located in the 5q region of the genome which is deleted in del(5q) interstitial deletion, a frequent deletion found in myeloid leukemias and myelodysplasias, suggesting that it may be a good candidate for the del(5q) tumor suppressor gene.

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: 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.