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Protein

Lysine-specific demethylase 3B

Gene

Kdm3b

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 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 (By similarity).By similarity

Cofactori

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

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi1361 – 13611Iron; catalyticPROSITE-ProRule annotation
Metal bindingi1363 – 13631Iron; catalyticPROSITE-ProRule annotation
Metal bindingi1490 – 14901Iron; catalyticPROSITE-ProRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri832 – 85726C6-typeSequence analysisAdd
BLAST

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

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
Gene namesi
Name:Kdm3b
Synonyms:Jhdm2b, Jmjd1b, Kiaa1082
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:1923356. Kdm3b.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 15621561Lysine-specific demethylase 3BPRO_0000234374Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei293 – 2931PhosphoserineBy similarity
Modified residuei347 – 3471PhosphoserineCombined sources
Modified residuei357 – 3571PhosphoserineCombined sources
Modified residuei361 – 3611PhosphoserineCombined sources
Modified residuei415 – 4151PhosphothreonineBy similarity
Modified residuei567 – 5671PhosphoserineBy similarity
Modified residuei574 – 5741PhosphoserineBy similarity
Modified residuei579 – 5791PhosphoserineBy similarity
Modified residuei599 – 5991PhosphoserineBy similarity
Modified residuei1054 – 10541PhosphoserineBy similarity
Modified residuei1060 – 10601PhosphoserineBy similarity

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiQ6ZPY7.
MaxQBiQ6ZPY7.
PaxDbiQ6ZPY7.
PeptideAtlasiQ6ZPY7.
PRIDEiQ6ZPY7.

PTM databases

iPTMnetiQ6ZPY7.
PhosphoSiteiQ6ZPY7.

Expressioni

Gene expression databases

CleanExiMM_JMJD1B.

Interactioni

Protein-protein interaction databases

BioGridi234928. 1 interaction.
STRINGi10090.ENSMUSP00000037628.

Structurei

3D structure databases

ProteinModelPortaliQ6ZPY7.
SMRiQ6ZPY7. Positions 1181-1521.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini1299 – 1522224JmjCPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi1094 – 10985LXXLL motif

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi255 – 545291Ser-richAdd
BLAST

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri832 – 85726C6-typeSequence analysisAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
InParanoidiQ6ZPY7.
PhylomeDBiQ6ZPY7.

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 (2)i

Sequence statusi: Complete.

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

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

Isoform 1 (identifier: Q6ZPY7-1) [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 KRLLLLFADP TASASASAPT AAAVVSGDPG PALRTRAWRA
60 70 80 90 100
GTVRAMSGAV PQDLAIFVEF DGCNWKQHSW VKVHAEDVLA LLLEGSLVWA
110 120 130 140 150
PRKDPVLLQG TRVPVAQWPA LTFTPLVDKL GLGSVVPVEY LVDRELRFLS
160 170 180 190 200
DANGMHLFQM GTDVQNQILL EHAALRETVN ALISDQKLQE IFSRGPYSVQ
210 220 230 240 250
GHRVKVYQPE GEEVWLCGVV SRQDSVTRLM EVSITETGEV KSVDPRLTHV
260 270 280 290 300
MLMDSSTPQS ENSRNSSLAS SGFGVSLSSL SQPLTFGSGR SQSNGVLATD
310 320 330 340 350
NKPLGFSFSC SSASESQKDS DLSKNLFFQC MSQNVPSTNY LSRVSESVAD
360 370 380 390 400
DSSSRDSFTQ SLESLTSGLC KGRSVLGADT QPGPKAGSSV DRKVPAESMP
410 420 430 440 450
TLTPAFPRSL LNTRTPENHE NLFLQPPKLS REEPSNPFLA FVEKVEHSPF
460 470 480 490 500
SSFVSQASGS SSSATSVTSK ATASWPESHS SAESAPLAKK KPLFITTDSS
510 520 530 540 550
KLVSGVLGSA LSTGSPSLSA VGNGRSSSPT NSLTQPIEMP TLSSSPTEER
560 570 580 590 600
PTVGPGQQDN PLLKTFSTVF GRHSGSFLSA PAEFAQENKA PFEAVKRFSL
610 620 630 640 650
DERSLACRQD SDSSTNSDLS DLSDSEEQLQ AKSGLKGIPE HLMGKLGPNG
660 670 680 690 700
ERSAELLLGK GKGKQAPKGR PRTAPLKVGQ SVLKDVSKVR KLKQSGEPFL
710 720 730 740 750
QDGSCINVAP HLHKCRECRL ERYRKFKEQE QDDSTVACRF FHFRRLVFTR
760 770 780 790 800
KGVLRVEGFL SPQQSDPDAM NLWIPSSSLA EGIDLETSKY ILANVGDQFC
810 820 830 840 850
QLVMSEKEAM MMVEPHQKVA WKRAVRGVRE MCDVCETTLF NIHWVCRKCG
860 870 880 890 900
FGVCLDCYRL RKSRPRSETE EMGDEEVFSW LKCAKGQSHE PENLMPTQII
910 920 930 940 950
PGTALYNIGD MVHAARGKWG IKANCPCISR QSKSVLRPAV TNGISQLPSV
960 970 980 990 1000
TPSASSGNET TFSSGGGAAA VTNPEPDQVP KGAGTDGRSE EPLKAEGSAS
1010 1020 1030 1040 1050
NSNSELKAIR PPCPDTAPPS SALHWLADLA TQKAKEETKD AGSLRSVLNK
1060 1070 1080 1090 1100
ESHSPFGLDS FNSTAKVSPL TPKLFNSLLL GPTASNSKTE GSSLRDLLHS
1110 1120 1130 1140 1150
GPGKLPQTPL DTGIPFPPVF SSSSAVAKSK ASLPDFLDHI IASVVENKKT
1160 1170 1180 1190 1200
SDPSKRSCNL TDTQKEVKEM AMGLNVLDPH TSHSWLCDGR LLCLHDPSNK
1210 1220 1230 1240 1250
NNWKIFRECW KQGQPVLVSG VHKKLKSELW KPEAFSQEFG DQDVDLVNCR
1260 1270 1280 1290 1300
NCAIISDVKV RDFWDGFEII CKRLRSEDGQ PMVLKLKDWP PGEDFRDMMP
1310 1320 1330 1340 1350
TRFEDLMENL PLPEYTKRDG RLNLASRLPS YFVRPDLGPK MYNAYGLITA
1360 1370 1380 1390 1400
EDRRVGTTNL HLDVSDAVNV MVYVGIPVGE GAHDEEVLKT IDEGDADEVT
1410 1420 1430 1440 1450
KQRIHDGKEK PGALWHIYAA KDAEKIRELL RKVGEEQGQE NPPDHDPIHD
1460 1470 1480 1490 1500
QSWYLDQILR KRLFEEYGVQ GWAIVQFLGD AVFIPAGAPH QVHNLYSCIK
1510 1520 1530 1540 1550
VAEDFVSPEH VKHCFRLTQE FRHLSNTHTN HEDKLQVKNI IYHAVKDAVG
1560
TLKAHESKLA RS
Length:1,562
Mass (Da):170,875
Last modified:May 16, 2006 - v2
Checksum:i4F2D7818104B50BE
GO
Isoform 2 (identifier: Q6ZPY7-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1070-1124: LTPKLFNSLL...PFPPVFSSSS → HVTSDLAHPR...YLVKNRFVVK
     1125-1562: Missing.

Note: No experimental confirmation available.
Show »
Length:1,124
Mass (Da):121,422
Checksum:i0E4EDA38840B35EA
GO

Sequence cautioni

The sequence AAH38376.1 differs from that shown. Reason: Frameshift at position 1555. Curated
The sequence BAC98091.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1126 – 11261V → G in AAH31981 (PubMed:15489334).Curated
Sequence conflicti1369 – 13702NV → SL in BAB31043 (PubMed:16141072).Curated
Sequence conflicti1545 – 15451V → G in BAB31043 (PubMed:16141072).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1070 – 112455LTPKL…FSSSS → HVTSDLAHPRRWGCSPSRTL HEHRSLQDPGRAHCFSQEAP GLGNVYLVKNRFVVK in isoform 2. 1 PublicationVSP_018301Add
BLAST
Alternative sequencei1125 – 1562438Missing in isoform 2. 1 PublicationVSP_018302Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129281 mRNA. Translation: BAC98091.1. Different initiation.
BC031981 mRNA. Translation: AAH31981.1.
BC038376 mRNA. Translation: AAH38376.1. Frameshift.
BC060727 mRNA. Translation: AAH60727.1.
BC108415 mRNA. Translation: AAI08416.1.
AK018027 mRNA. Translation: BAB31043.1.
AK033343 mRNA. Translation: BAC28239.1.
RefSeqiXP_006526040.1. XM_006525977.2. [Q6ZPY7-1]
UniGeneiMm.277906.

Genome annotation databases

GeneIDi277250.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK129281 mRNA. Translation: BAC98091.1. Different initiation.
BC031981 mRNA. Translation: AAH31981.1.
BC038376 mRNA. Translation: AAH38376.1. Frameshift.
BC060727 mRNA. Translation: AAH60727.1.
BC108415 mRNA. Translation: AAI08416.1.
AK018027 mRNA. Translation: BAB31043.1.
AK033343 mRNA. Translation: BAC28239.1.
RefSeqiXP_006526040.1. XM_006525977.2. [Q6ZPY7-1]
UniGeneiMm.277906.

3D structure databases

ProteinModelPortaliQ6ZPY7.
SMRiQ6ZPY7. Positions 1181-1521.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi234928. 1 interaction.
STRINGi10090.ENSMUSP00000037628.

PTM databases

iPTMnetiQ6ZPY7.
PhosphoSiteiQ6ZPY7.

Proteomic databases

EPDiQ6ZPY7.
MaxQBiQ6ZPY7.
PaxDbiQ6ZPY7.
PeptideAtlasiQ6ZPY7.
PRIDEiQ6ZPY7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi277250.

Organism-specific databases

CTDi51780.
MGIiMGI:1923356. Kdm3b.
RougeiSearch...

Phylogenomic databases

eggNOGiKOG1356. Eukaryota.
ENOG410XTAA. LUCA.
InParanoidiQ6ZPY7.
PhylomeDBiQ6ZPY7.

Miscellaneous databases

PROiQ6ZPY7.
SOURCEiSearch...

Gene expression databases

CleanExiMM_JMJD1B.

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...

Publicationsi

  1. "Prediction of the coding sequences of mouse homologues of KIAA gene: III. The complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries."
    Okazaki N., Kikuno R., Ohara R., Inamoto S., Koseki H., Hiraoka S., Saga Y., Nagase T., Ohara O., Koga H.
    DNA Res. 10:167-180(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
    Tissue: Embryonic tail.
  2. "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 574-1562 (ISOFORM 1).
    Strain: C57BL/6J and Czech II.
    Tissue: Brain, Eye and Mammary tumor.
  3. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1119-1562.
    Strain: C57BL/6J.
    Tissue: Testis and Thymus.
  4. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-347; SER-357 AND SER-361, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Brain, Heart, Kidney, Lung, Spleen and Testis.

Entry informationi

Entry nameiKDM3B_MOUSE
AccessioniPrimary (citable) accession number: Q6ZPY7
Secondary accession number(s): Q2VPQ5
, Q5U5V7, Q6P9K3, Q8CCE2, Q8K2A5, Q9CU57
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 16, 2006
Last sequence update: May 16, 2006
Last modified: July 6, 2016
This is version 89 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.