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Lysine-specific histone demethylase 1B (EC 1.-.-.-) (Flavin-containing amine oxidase domain-containing protein 1) (Lysine-specific histone demethylase 2)

 KDM1B_MOUSE             Reviewed;         826 AA.
Q8CIG3; Q8C5C4; Q8CEC1;
25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
01-MAR-2003, sequence version 1.
22-NOV-2017, entry version 117.
RecName: Full=Lysine-specific histone demethylase 1B;
EC=1.-.-.-;
AltName: Full=Flavin-containing amine oxidase domain-containing protein 1;
AltName: Full=Lysine-specific histone demethylase 2;
Name=Kdm1b; Synonyms=Aof1, Lsd2;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), AND NUCLEOTIDE
SEQUENCE [LARGE SCALE MRNA] OF 285-826 (ISOFORM 2).
STRAIN=C57BL/6J; TISSUE=Cecum, and Skin;
PubMed=16141072; DOI=10.1126/science.1112014;
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.;
"The transcriptional landscape of the mammalian genome.";
Science 309:1559-1563(2005).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=FVB/N; TISSUE=Mammary tumor;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[3]
FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND ENZYME
REGULATION.
PubMed=19407342; DOI=10.1074/jbc.M109.003087;
Karytinos A., Forneris F., Profumo A., Ciossani G., Battaglioli E.,
Binda C., Mattevi A.;
"A novel mammalian flavin-dependent histone demethylase.";
J. Biol. Chem. 284:17775-17782(2009).
[4]
FUNCTION, MUTAGENESIS OF LYS-667, SUBCELLULAR LOCATION, TISSUE
SPECIFICITY, AND DISRUPTION PHENOTYPE.
PubMed=19727073; DOI=10.1038/nature08315;
Ciccone D.N., Su H., Hevi S., Gay F., Lei H., Bajko J., Xu G., Li E.,
Chen T.;
"KDM1B is a histone H3K4 demethylase required to establish maternal
genomic imprints.";
Nature 461:415-418(2009).
[5]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17 AND SER-253, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Kidney, Pancreas, and Spleen;
PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
"A tissue-specific atlas of mouse protein phosphorylation and
expression.";
Cell 143:1174-1189(2010).
-!- FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone
H3, a specific tag for epigenetic transcriptional activation,
thereby acting as a corepressor. Required for de novo DNA
methylation of a subset of imprinted genes during oogenesis. Acts
by oxidizing the substrate by FAD to generate the corresponding
imine that is subsequently hydrolyzed. Demethylates both mono- and
di-methylated 'Lys-4' of histone H3. Has no effect on tri-
methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-,
di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-
36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of
histone H4. {ECO:0000269|PubMed:19407342,
ECO:0000269|PubMed:19727073}.
-!- COFACTOR:
Name=FAD; Xref=ChEBI:CHEBI:57692;
Evidence={ECO:0000269|PubMed:19407342};
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000250|UniProtKB:Q8NB78};
Note=Binds 3 Zn(2+) ions per subunit.
{ECO:0000250|UniProtKB:Q8NB78};
-!- ENZYME REGULATION: Inhibited by tranylcypromine, but not by
pargyline, deprenyl or rasagiline (PubMed:19407342). Histone
H3K4me1 and H3K4me2 demethylase activity is enhanced by GLYR1 (By
similarity). {ECO:0000250|UniProtKB:Q8NB78,
ECO:0000269|PubMed:19407342}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=9.2 uM for mono-methylated 'Lys-4' histone H3 N-terminal
peptide {ECO:0000269|PubMed:19407342};
KM=11.3 uM for di-methylated 'Lys-4' histone H3 N-terminal
peptide {ECO:0000269|PubMed:19407342};
KM=9.0 uM for mono-methylated 'Lys-4', mono-methylated 'Lys-9'
histone H3 N-terminal peptide {ECO:0000269|PubMed:19407342};
KM=6.6 uM for di-methylated 'Lys-4', di-methylated 'Lys-9'
histone H3 N-terminal peptide {ECO:0000269|PubMed:19407342};
KM=70.5 uM for mono-methylated 'Lys-4', acetylated 'Lys-9'
histone H3 N-terminal peptide {ECO:0000269|PubMed:19407342};
KM=8.1 uM for mono-methylated 'Lys-4', mono-methylated 'Arg-17'
histone H3 N-terminal peptide {ECO:0000269|PubMed:19407342};
pH dependence:
Optimum pH is 8.5. {ECO:0000269|PubMed:19407342};
-!- SUBUNIT: Interacts with its cofactor GLYR1 at nucleosomes; this
interaction stimulates H3K4me1 and H3K4me2 demethylation (By
similarity). Does not form a complex with RCOR1/CoREST.
{ECO:0000250|UniProtKB:Q8NB78}.
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:19727073}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=3;
Name=1;
IsoId=Q8CIG3-1; Sequence=Displayed;
Name=2;
IsoId=Q8CIG3-2; Sequence=VSP_019969;
Note=No experimental confirmation available.;
Name=3;
IsoId=Q8CIG3-3; Sequence=VSP_019968;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Expressed in growing oocytes and in intestinal
gland. {ECO:0000269|PubMed:19727073}.
-!- DOMAIN: The SWIRM domain may act as an anchor site for a histone
tail. {ECO:0000250}.
-!- DISRUPTION PHENOTYPE: No effect on mouse development and
oogenesis, but embryos derived from oocytes from Kdm1b-deficient
females die before mid-gestation. {ECO:0000269|PubMed:19727073}.
-!- MISCELLANEOUS: Acetylation of 'Lys-9' decreases the binding of the
substrate, while hyperacetylation of 'Lys-9', 'Lys-14' and 'Lys-
18', phosphorylation of 'Thr3' or 'Ser-10', and methylation of
'Arg-2' or 'Arg-8' abolishes its binding. Methylation of 'Lys-9'
and 'Arg-17' are the only two epigenetic modifications that have
no significant effect on catalysis.
-!- SIMILARITY: Belongs to the flavin monoamine oxidase family.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAC26005.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
Sequence=BAC37460.1; Type=Frameshift; Positions=825; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; AK028553; BAC26005.1; ALT_INIT; mRNA.
EMBL; AK078920; BAC37460.1; ALT_FRAME; mRNA.
EMBL; BC023917; AAH23917.1; -; mRNA.
CCDS; CCDS26489.1; -. [Q8CIG3-1]
RefSeq; NP_758466.1; NM_172262.3. [Q8CIG3-1]
UniGene; Mm.31259; -.
ProteinModelPortal; Q8CIG3; -.
SMR; Q8CIG3; -.
BioGrid; 230002; 1.
DIP; DIP-59111N; -.
STRING; 10090.ENSMUSP00000038373; -.
iPTMnet; Q8CIG3; -.
PhosphoSitePlus; Q8CIG3; -.
EPD; Q8CIG3; -.
PaxDb; Q8CIG3; -.
PeptideAtlas; Q8CIG3; -.
PRIDE; Q8CIG3; -.
Ensembl; ENSMUST00000037025; ENSMUSP00000038373; ENSMUSG00000038080. [Q8CIG3-1]
GeneID; 218214; -.
KEGG; mmu:218214; -.
UCSC; uc007qht.3; mouse. [Q8CIG3-1]
UCSC; uc007qhu.3; mouse. [Q8CIG3-2]
UCSC; uc011yyy.2; mouse. [Q8CIG3-3]
CTD; 221656; -.
MGI; MGI:2145261; Kdm1b.
eggNOG; KOG0029; Eukaryota.
eggNOG; ENOG410XSNC; LUCA.
GeneTree; ENSGT00530000062888; -.
HOGENOM; HOG000230870; -.
InParanoid; Q8CIG3; -.
KO; K19413; -.
OMA; PFYQPNE; -.
OrthoDB; EOG091G04NO; -.
PhylomeDB; Q8CIG3; -.
TreeFam; TF352593; -.
Reactome; R-MMU-3214842; HDMs demethylate histones.
Reactome; R-MMU-5689603; UCH proteinases.
ChiTaRS; Kdm1b; mouse.
PRO; PR:Q8CIG3; -.
Proteomes; UP000000589; Chromosome 13.
Bgee; ENSMUSG00000038080; -.
CleanEx; MM_AOF1; -.
ExpressionAtlas; Q8CIG3; baseline and differential.
Genevisible; Q8CIG3; MM.
GO; GO:0000786; C:nucleosome; IEA:Ensembl.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0071949; F:FAD binding; ISS:UniProtKB.
GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:UniProtKB.
GO; GO:0042393; F:histone binding; IEA:Ensembl.
GO; GO:0034648; F:histone demethylase activity (H3-dimethyl-K4 specific); IDA:UniProtKB.
GO; GO:0034649; F:histone demethylase activity (H3-monomethyl-K4 specific); IDA:UniProtKB.
GO; GO:0008270; F:zinc ion binding; IDA:UniProtKB.
GO; GO:0043046; P:DNA methylation involved in gamete generation; IMP:MGI.
GO; GO:0034720; P:histone H3-K4 demethylation; IDA:UniProtKB.
GO; GO:0007275; P:multicellular organism development; IEA:UniProtKB-KW.
GO; GO:0044030; P:regulation of DNA methylation; IMP:UniProtKB.
GO; GO:0006349; P:regulation of gene expression by genetic imprinting; IMP:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
Gene3D; 1.10.10.10; -; 1.
Gene3D; 3.50.50.60; -; 1.
InterPro; IPR002937; Amino_oxidase.
InterPro; IPR036188; FAD/NAD-bd_sf.
InterPro; IPR009057; Homeobox-like_sf.
InterPro; IPR007526; SWIRM.
InterPro; IPR036388; WH-like_DNA-bd_sf.
InterPro; IPR011124; Znf_CW.
Pfam; PF01593; Amino_oxidase; 1.
Pfam; PF04433; SWIRM; 1.
Pfam; PF07496; zf-CW; 1.
SUPFAM; SSF46689; SSF46689; 1.
SUPFAM; SSF51905; SSF51905; 2.
PROSITE; PS50934; SWIRM; 1.
PROSITE; PS51050; ZF_CW; 1.
1: Evidence at protein level;
Alternative splicing; Chromatin regulator; Complete proteome;
Developmental protein; FAD; Flavoprotein; Metal-binding; Nucleus;
Oxidoreductase; Phosphoprotein; Reference proteome; Repressor;
Transcription; Transcription regulation; Zinc; Zinc-finger.
CHAIN 1 826 Lysine-specific histone demethylase 1B.
/FTId=PRO_0000247337.
DOMAIN 281 379 SWIRM. {ECO:0000255|PROSITE-
ProRule:PRU00247}.
ZN_FING 133 193 CW-type. {ECO:0000255|PROSITE-
ProRule:PRU00454}.
NP_BIND 389 445 FAD. {ECO:0000250|UniProtKB:Q8NB78,
ECO:0000255}.
NP_BIND 807 809 FAD. {ECO:0000250|UniProtKB:Q8NB78}.
REGION 279 298 GLYR1-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
REGION 444 473 Histone H3-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
REGION 493 504 Histone H3-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
REGION 544 578 Histone H3-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
REGION 570 572 GLYR1-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
REGION 802 818 GLYR1-binding.
{ECO:0000250|UniProtKB:Q8NB78}.
METAL 53 53 Zinc 1. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 58 58 Zinc 1. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 65 65 Zinc 2. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 73 73 Zinc 2. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 84 84 Zinc 1; via pros nitrogen.
{ECO:0000250|UniProtKB:Q8NB78}.
METAL 90 90 Zinc 1; via tele nitrogen.
{ECO:0000250|UniProtKB:Q8NB78}.
METAL 92 92 Zinc 2. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 95 95 Zinc 2. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 142 142 Zinc 3. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 147 147 Zinc 3. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 169 169 Zinc 3. {ECO:0000250|UniProtKB:Q8NB78}.
METAL 185 185 Zinc 3. {ECO:0000250|UniProtKB:Q8NB78}.
BINDING 604 604 FAD; via amide nitrogen and carbonyl
oxygen. {ECO:0000250|UniProtKB:Q8NB78}.
BINDING 799 799 FAD; via amide nitrogen.
{ECO:0000250|UniProtKB:Q8NB78}.
MOD_RES 17 17 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
MOD_RES 26 26 Phosphoserine.
{ECO:0000250|UniProtKB:Q8NB78}.
MOD_RES 253 253 Phosphoserine.
{ECO:0000244|PubMed:21183079}.
VAR_SEQ 1 621 Missing (in isoform 3).
{ECO:0000303|PubMed:16141072}.
/FTId=VSP_019968.
VAR_SEQ 459 558 Missing (in isoform 2).
{ECO:0000303|PubMed:16141072}.
/FTId=VSP_019969.
MUTAGEN 667 667 K->A: Loss of activity.
{ECO:0000269|PubMed:19727073}.
SEQUENCE 826 AA; 92633 MW; 02FD6FE991B1C030 CRC64;
MAASRGRSKK RSNLELSPDN LPLRSSGRQA KKKAVEIPDE DEDGSSEKKY RKCEKAGCTA
AYPVCFASAS ERCAKNGYTS RWYHLSCGEH FCNECFDHYY RSHKDGYDKY SAWKRVWTSN
GKTEPSPKAF MADQQLPYWV QCTKPECGKW RQLTKEIQLT PHMARTYRCG MKPNTITKPD
TPDHCSFPED LRVLEVSNHW WYPMLIQPPL LKDSVAAPLL SAYYPDCVGM SPSCTSTHRA
TVTAATTTTG SASPGEMEPS KAAPSSLVLG MNRYFQPFYQ PNECGKALCV RPDVMELDEL
YEFPEYSRDP TMYLALRNLI LALWYTNCKE ALTPQKCIPH IIVRGLVRIR CVQEVERILY
FMTRKGLINT GVLTVAAGQH LLPKHYHNKS VLVVGAGPAG LAAARQLHNF GMKVTVLEAK
DRIGGRVWDD KSFKGVVVGR GPQIVNGCIN NPVALMCEQL GISMRKLGER CDLIQEGGRI
TDPTVDKRMD FHFNALLDVV SEWRKDKTLL QDVPLGEKIE EIYRAFVKES GIQFSELEGQ
VLQFHLSNLE YACGSSLHQV SARSWDHNEF FAQFAGDHTL LTPGYSTIIE KLAEGLDIRL
KSPVQSIDYT GDEVQVTTTD GMGHSAQKVL VTVPLAILQR GAIQFNPPLS EKKMKAINSL
GAGIIEKIAL QFPYRFWDSK VQGADFFGHV PPSASQRGLF AVFYDMDSQQ SVLMSVITGE
AVASLRTMDD KQVLQQCMGI LRELFKEQEI PEPTKYFVTR WSTEPWIQMA YSFVKTFGSG
EAYDIIAEEI QGTVFFAGEA TNRHFPQTVT GAYLSGVREA SKIAAF


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