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Q7LBC6 (KDM3B_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 88. 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·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:KDM3B
Synonyms:C5orf7, JHDM2B, JMJD1B, KIAA1082
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1761 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.8

Cofactor

Binds 1 Fe2+ ion per subunit By similarity.

Subcellular location

Nucleus By similarity.

Tissue specificity

Ubiquitous. Highly expressed in placenta, skeletal muscle, kidney, heart and liver. Ref.1 Ref.2

Domain

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

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.

Sequence similarities

Belongs to the JHDM2 histone demethylase family.

Contains 1 JmjC domain.

Sequence caution

The sequence BAA83034.2 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q7LBC6-1)

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.
Isoform 2 (identifier: Q7LBC6-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-344: Missing.
     345-349: TFVPQ → MGAME
Isoform 3 (identifier: Q7LBC6-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1002: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Initiator methionine11Removed Ref.11
Chain2 – 17611760Lysine-specific demethylase 3B
PRO_0000234373

Regions

Domain1498 – 1721224JmjC
Zinc finger1031 – 105626C6-type Potential
Motif1293 – 12975LXXLL motif
Compositional bias647 – 74498Ser-rich

Sites

Metal binding15601Iron; catalytic By similarity
Metal binding15621Iron; catalytic By similarity
Metal binding16891Iron; catalytic By similarity

Amino acid modifications

Modified residue21N-acetylalanine Ref.11 Ref.16
Modified residue3611N6-acetyllysine Ref.13
Modified residue7731Phosphoserine Ref.10 Ref.14
Modified residue7791Phosphoserine Ref.10 Ref.14
Modified residue7981Phosphoserine Ref.9 Ref.14

Natural variations

Alternative sequence1 – 10021002Missing in isoform 3.
VSP_018298
Alternative sequence1 – 344344Missing in isoform 2.
VSP_018299
Alternative sequence345 – 3495TFVPQ → MGAME in isoform 2.
VSP_018300
Natural variant2561A → T. Ref.2 Ref.3 Ref.6 Ref.7
Corresponds to variant rs6865472 [ dbSNP | Ensembl ].
VAR_026221
Natural variant12011S → N.
Corresponds to variant rs7706614 [ dbSNP | Ensembl ].
VAR_026222

Experimental info

Sequence conflict5691C → R in AAF63765. Ref.1

Secondary structure

.................................................................. 1761
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified October 5, 2010. Version 2.
Checksum: FB900FCBF0675CD8

FASTA1,761191,581
        10         20         30         40         50         60 
MADAAASPVG KRLLLLFADT AASASASAPA AAAASGDPGP ALRTRAWRAG TVRAMSGAVP 

        70         80         90        100        110        120 
QDLAIFVEFD GCNWKQHSWV KVHAEEVIVL LLEGSLVWAP REDPVLLQGI RVSIAQWPAL 

       130        140        150        160        170        180 
TFTPLVDKLG LGSVVPVEYL LDRELRFLSD ANGLHLFQMG TDSQNQILLE HAALRETVNA 

       190        200        210        220        230        240 
LISDQKLQEI FSRGPYSVQG HRVKIYQPEG EEGWLYGVVS HQDSITRLME VSVTESGEIK 

       250        260        270        280        290        300 
SVDPRLIHVM LMDNSAPQSE GGTLKAVKSS KGKKKRESIE GKDGRRRKSA SDSGCDPASK 

       310        320        330        340        350        360 
KLKGDRGEVD SNGSDGGEAS RGPWKGGNAS GEPGLDQRAK QPPSTFVPQI NRNIRFATYT 

       370        380        390        400        410        420 
KENGRTLVVQ DEPVGGDTPA SFTPYSTATG QTPLAPEVGG AENKEAGKTL EQVGQGIVAS 

       430        440        450        460        470        480 
AAVVTTASST PNTVRISDTG LAAGTVPEKQ KGSRSQASGE NSRNSILASS GFGAPLPSSS 

       490        500        510        520        530        540 
QPLTFGSGRS QSNGVLATEN KPLGFSFGCS SAQEAQKDTD LSKNLFFQCM SQTLPTSNYF 

       550        560        570        580        590        600 
TTVSESLADD SSSRDSFKQS LESLSSGLCK GRSVLGTDTK PGSKAGSSVD RKVPAESMPT 

       610        620        630        640        650        660 
LTPAFPRSLL NARTPENHEN LFLQPPKLSR EEPSNPFLAF VEKVEHSPFS SFASQASGSS 

       670        680        690        700        710        720 
SSATTVTSKV APSWPESHSS ADSASLAKKK PLFITTDSSK LVSGVLGSAL TSGGPSLSAM 

       730        740        750        760        770        780 
GNGRSSSPTS SLTQPIEMPT LSSSPTEERP TVGPGQQDNP LLKTFSNVFG RHSGGFLSSP 

       790        800        810        820        830        840 
ADFSQENKAP FEAVKRFSLD ERSLACRQDS DSSTNSDLSD LSDSEEQLQA KTGLKGIPEH 

       850        860        870        880        890        900 
LMGKLGPNGE RSAELLLGKS KGKQAPKGRP RTAPLKVGQS VLKDVSKVKK LKQSGEPFLQ 

       910        920        930        940        950        960 
DGSCINVAPH LHKCRECRLE RYRKFKEQEQ DDSTVACRFF HFRRLIFTRK GVLRVEGFLS 

       970        980        990       1000       1010       1020 
PQQSDPDAMN LWIPSSSLAE GIDLETSKYI LANVGDQFCQ LVMSEKEAMM MVEPHQKVAW 

      1030       1040       1050       1060       1070       1080 
KRAVRGVREM CDVCETTLFN IHWVCRKCGF GVCLDCYRLR KSRPRSETEE MGDEEVFSWL 

      1090       1100       1110       1120       1130       1140 
KCAKGQSHEP ENLMPTQIIP GTALYNIGDM VHAARGKWGI KANCPCISRQ NKSVLRPAVT 

      1150       1160       1170       1180       1190       1200 
NGMSQLPSIN PSASSGNETT FSGGGGPAPV TTPEPDHVPK ADSTDIRSEE PLKTDSSASN 

      1210       1220       1230       1240       1250       1260 
SNSELKAIRP PCPDTAPPSS ALHWLADLAT QKAKEETKEA GSLRSVLNKE SHSPFGLDSF 

      1270       1280       1290       1300       1310       1320 
NSTAKVSPLT PKLFNSLLLG PTASNNKTEG SSLRDLLHSG PGKLPQTPLD TGIPFPPVFS 

      1330       1340       1350       1360       1370       1380 
TSSAGVKSKA SLPNFLDHII ASVVENKKTS DASKRACNLT DTQKEVKEMV MGLNVLDPHT 

      1390       1400       1410       1420       1430       1440 
SHSWLCDGRL LCLHDPSNKN NWKIFRECWK QGQPVLVSGV HKKLKSELWK PEAFSQEFGD 

      1450       1460       1470       1480       1490       1500 
QDVDLVNCRN CAIISDVKVR DFWDGFEIIC KRLRSEDGQP MVLKLKDWPP GEDFRDMMPT 

      1510       1520       1530       1540       1550       1560 
RFEDLMENLP LPEYTKRDGR LNLASRLPSY FVRPDLGPKM YNAYGLITAE DRRVGTTNLH 

      1570       1580       1590       1600       1610       1620 
LDVSDAVNVM VYVGIPIGEG AHDEEVLKTI DEGDADEVTK QRIHDGKEKP GALWHIYAAK 

      1630       1640       1650       1660       1670       1680 
DAEKIRELLR KVGEEQGQEN PPDHDPIHDQ SWYLDQTLRK RLYEEYGVQG WAIVQFLGDA 

      1690       1700       1710       1720       1730       1740 
VFIPAGAPHQ VHNLYSCIKV AEDFVSPEHV KHCFRLTQEF RHLSNTHTNH EDKLQVKNII 

      1750       1760 
YHAVKDAVGT LKAHESKLAR S 

« Hide

Isoform 2 [UniParc].

Checksum: AF66C2E416D31F40
Show »

FASTA1,417154,668
Isoform 3 [UniParc].

Checksum: 5A13F19C0EE952EF
Show »

FASTA75984,712

References

« Hide 'large scale' references
[1]"cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins."
Lai F., Godley L.A., Fernald A.A., Orelli B.J., Pamintuan L., Zhao N., Le Beau M.M.
Genomics 70:123-130(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), TISSUE SPECIFICITY.
Tissue: Bone marrow.
[2]"A novel nuclear protein, 5qNCA (LOC51780) is a candidate for the myeloid leukemia tumor suppressor gene on chromosome 5 band q31."
Hu Z., Gomes I., Horrigan S.K., Kravarusic J., Mar B., Arbieva Z., Chyna B., Fulton N., Edassery S., Raza A., Westbrook C.A.
Oncogene 20:6946-6954(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANT THR-256.
[3]"Prediction of the coding sequences of unidentified human genes. XIV. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Kikuno R., Nagase T., Ishikawa K., Hirosawa M., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 6:197-205(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT THR-256.
Tissue: Brain.
[4]"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.
[5]"The DNA sequence and comparative analysis of human chromosome 5."
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S. expand/collapse author list , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], VARIANT THR-256.
[7]"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] (ISOFORMS 1 AND 3), VARIANT THR-256.
Tissue: Brain and Eye.
[8]"JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor."
Yamane K., Toumazou C., Tsukada Y.I., Erdjument-Bromage H., Tempst P., Wong J., Zhang Y.
Cell 125:483-495(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY.
[9]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-798, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-773 AND SER-779, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach."
Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.
Anal. Chem. 81:4493-4501(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS], CLEAVAGE OF INITIATOR METHIONINE [LARGE SCALE ANALYSIS].
[12]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[13]"Lysine acetylation targets protein complexes and co-regulates major cellular functions."
Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-361, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-773; SER-779 AND SER-798, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[15]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"N-terminal acetylome analyses and functional insights of the N-terminal acetyltransferase NatB."
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A., Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
RefSeqNP_057688.2. NM_016604.3.
UniGeneHs.483486.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
4C8DX-ray2.18A1380-1720[»]
ProteinModelPortalQ7LBC6.
SMRQ7LBC6. Positions 1000-1058, 1380-1720.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid119727. 13 interactions.
IntActQ7LBC6. 3 interactions.
MINTMINT-1195273.
STRING9606.ENSP00000326563.

PTM databases

PhosphoSiteQ7LBC6.

Polymorphism databases

DMDM308153456.

Proteomic databases

PaxDbQ7LBC6.
PRIDEQ7LBC6.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000314358; ENSP00000326563; ENSG00000120733. [Q7LBC6-1]
ENST00000394866; ENSP00000378335; ENSG00000120733. [Q7LBC6-2]
GeneID51780.
KEGGhsa:51780.
UCSCuc003lcy.1. human. [Q7LBC6-1]
uc010jew.1. human. [Q7LBC6-2]

Organism-specific databases

CTD51780.
GeneCardsGC05P137688.
HGNCHGNC:1337. KDM3B.
HPAHPA016610.
MIM609373. gene.
neXtProtNX_Q7LBC6.
PharmGKBPA25918.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG305537.
InParanoidQ7LBC6.
KOK15601.
OMAIICKRLR.
PhylomeDBQ7LBC6.
TreeFamTF324723.

Gene expression databases

ArrayExpressQ7LBC6.
BgeeQ7LBC6.
CleanExHS_JMJD1B.
GenevestigatorQ7LBC6.

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

GeneWikiJMJD1B.
GenomeRNAi51780.
NextBio55912.
PROQ7LBC6.
SOURCESearch...

Entry information

Entry nameKDM3B_HUMAN
AccessionPrimary (citable) accession number: Q7LBC6
Secondary accession number(s): A6H8X7 expand/collapse secondary AC list , Q9BVH6, Q9BW93, Q9BZ52, Q9NYF4, Q9UPS0
Entry history
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: October 5, 2010
Last modified: April 16, 2014
This is version 88 of the entry and version 2 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 5

Human chromosome 5: entries, gene names and cross-references to MIM