ID A0A0R4ISI0_DANRE Unreviewed; 1777 AA.
AC A0A0R4ISI0; A0A8M2BKF5;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JUN-2018, sequence version 3.
DT 27-MAR-2024, entry version 49.
DE RecName: Full=Lysine-specific demethylase {ECO:0000256|RuleBase:RU369087};
DE EC=1.14.11.65 {ECO:0000256|RuleBase:RU369087};
GN Name=kdm3b {ECO:0000313|Ensembl:ENSDARP00000138150,
GN ECO:0000313|RefSeq:XP_005173198.1,
GN ECO:0000313|ZFIN:ZDB-GENE-101007-4};
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955 {ECO:0000313|Ensembl:ENSDARP00000138150};
RN [1] {ECO:0000313|Ensembl:ENSDARP00000138150, ECO:0000313|Proteomes:UP000000437}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000138150};
RX PubMed=23594743; DOI=10.1038/nature12111;
RG Genome Reference Consortium Zebrafish;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Eliott D.,
RA Threadgold G., Harden G., Ware D., Begum S., Mortimore B., Mortimer B.,
RA Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M.,
RA Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M.,
RA Glithero R., Howden P., Barker N., Lloyd C., Stevens C., Harley J.,
RA Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D.,
RA Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K.,
RA Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R.,
RA Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M.,
RA Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D.,
RA Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M.,
RA Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M.,
RA Woodmansey R., Clark G., Cooper J., Cooper J., Tromans A., Grafham D.,
RA Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J.,
RA Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I.,
RA Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M.,
RA Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M.,
RA Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G., Osoegawa K., Zhu B.,
RA Rapp A., Widaa S., Langford C., Yang F., Schuster S.C., Carter N.P.,
RA Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R.,
RA Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I.,
RA Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H.,
RA Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [2] {ECO:0000313|Ensembl:ENSDARP00000138150}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|Ensembl:ENSDARP00000138150};
RG Ensembl;
RL Submitted (NOV-2015) to UniProtKB.
RN [3] {ECO:0000313|RefSeq:XP_005173198.1}
RP IDENTIFICATION.
RC STRAIN=Tuebingen {ECO:0000313|RefSeq:XP_005173198.1};
RG RefSeq;
RL Submitted (NOV-2023) to UniProtKB.
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-9' of
CC histone H3, thereby playing a central role in histone code.
CC {ECO:0000256|RuleBase:RU369087}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(6),N(6)-dimethyl-L-lysyl(9)-[histone H3]
CC + 2 O2 = 2 CO2 + 2 formaldehyde + L-lysyl(9)-[histone H3] + 2
CC succinate; Xref=Rhea:RHEA:60188, Rhea:RHEA-COMP:15541, Rhea:RHEA-
CC COMP:15546, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:29969, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:61976; EC=1.14.11.65;
CC Evidence={ECO:0000256|RuleBase:RU369087};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000256|RuleBase:RU369087};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000256|RuleBase:RU369087};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000256|ARBA:ARBA00004123,
CC ECO:0000256|RuleBase:RU369087}.
CC -!- DOMAIN: Leu-Xaa-Xaa-Leu-Leu (LXXLL) motifs are known to mediate the
CC association with nuclear receptors. {ECO:0000256|RuleBase:RU369087}.
CC -!- DOMAIN: The JmjC domain and the C6-type zinc-finger are required for
CC the demethylation activity. {ECO:0000256|RuleBase:RU369087}.
CC -!- SIMILARITY: Belongs to the JHDM2 histone demethylase family.
CC {ECO:0000256|RuleBase:RU369087}.
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DR EMBL; CR854933; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CT573790; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; XP_005173198.1; XM_005173141.4.
DR PaxDb; 7955-ENSDARP00000084278; -.
DR Ensembl; ENSDART00000172442; ENSDARP00000138150; ENSDARG00000062267.
DR Ensembl; ENSDART00000172442.3; ENSDARP00000138150.3; ENSDARG00000062267.7.
DR GeneID; 326643; -.
DR AGR; ZFIN:ZDB-GENE-101007-4; -.
DR CTD; 51780; -.
DR ZFIN; ZDB-GENE-101007-4; kdm3b.
DR OrthoDB; 3473445at2759; -.
DR Proteomes; UP000000437; Chromosome 14.
DR Bgee; ENSDARG00000062267; Expressed in mature ovarian follicle and 27 other cell types or tissues.
DR GO; GO:0000785; C:chromatin; IBA:GO_Central.
DR GO; GO:0000118; C:histone deacetylase complex; IBA:GO_Central.
DR GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR GO; GO:0032454; F:histone H3K9 demethylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003712; F:transcription coregulator activity; IBA:GO_Central.
DR GO; GO:0070988; P:demethylation; IEA:UniProtKB-UniRule.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR Gene3D; 2.60.120.650; Cupin; 1.
DR InterPro; IPR045109; JHDM2-like.
DR InterPro; IPR003347; JmjC_dom.
DR PANTHER; PTHR12549; JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN; 1.
DR PANTHER; PTHR12549:SF8; LYSINE-SPECIFIC DEMETHYLASE 3B; 1.
DR Pfam; PF02373; JmjC; 1.
DR SMART; SM00558; JmjC; 1.
DR SUPFAM; SSF51197; Clavaminate synthase-like; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 1: Evidence at protein level;
KW Iron {ECO:0000256|RuleBase:RU369087};
KW Metal-binding {ECO:0000256|RuleBase:RU369087};
KW Nucleus {ECO:0000256|RuleBase:RU369087};
KW Proteomics identification {ECO:0007829|PeptideAtlas:A0A0R4ISI0};
KW Reference proteome {ECO:0000313|Proteomes:UP000000437}.
FT DOMAIN 1506..1737
FT /note="JmjC"
FT /evidence="ECO:0000259|PROSITE:PS51184"
FT REGION 247..314
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 345..506
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 690..734
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 757..787
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 803..870
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1116..1318
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 249..287
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 408..449
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 465..483
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 691..719
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 757..784
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 809..829
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1118..1152
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1166..1190
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1191..1220
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1261..1280
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1297..1311
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 1777 AA; 192303 MW; F1A1F25D0F74A669 CRC64;
MGDSLGLIGK RLLLLLNDGS SAPAATGGEV ERAAWLRGTV RAVSVIGLAS PGVEVFVEFE
DSPWRKRAWV QLYGDEVRVV LMESAIVWAN CSDPSLSTAL GSSATQWPAL MFKQLIDRVG
LGSVVPVEFF GARNLAFLPN GNSLHTFETE KDFTHSLLQE QPALQHAISS WHTDSELQEI
LRKGSYTIQG RRVKVYQPEF EQPWAFGLVS QHDPVSHIME ITMDQSCLKG EETQVVDPRV
IHVMLAEGKL NESQDRRKKE GDGGKGEGSR RRRTASEGDE DITLKRFKGA GEGASDNQNG
NSSNRDAEAM QEHSHIRSTG FVKENGSFIP NQERISSVSA VLPASTPTPP PLKPAPSPFS
NTFPSLGQMP NLVPGAPAPK SSPTLPSSER EEGGVLSGYP KTAALVSPGP VTISSPSQEN
TSSVALTAPV DANQKPSMWG STSEGNQTPK APVLAPAGFG KQSSGGVFGN VSTQTNGSSQ
GDKPFGFSFR GAKDSQRQDS DTSQNLFFQF ISQNQSNTQG QSKAFTSLSE CLNKEPPSLF
KSAAPSEGFK KTVVASASTG LFGSAPASGL APLKEQPKVP DIKPAGNGIL MNKPFGAVGE
AQSKLPATFS SAIIQAASST EVLKPSGLGT SGLGNASGGI RNVNSSTPVS SFGLLAGNKV
SDGHENLFLQ PSKETNSFLA YGRGVPQTPF GALTSPKSSS AQSASAVSPS GSTSLLGQDP
PGSDAKPNLF TMAEPPKGIL APQFAAPALM TTPSFTSVAQ DGQQISKPNR EGSDDSSGTL
LSTEAEGVSV PFEQSKFSLE ERLQSIKKDS ESSSNSDLSD LSEGEDNAGQ SQKPDLPAGN
EDKNKAQAAA KSRPRSKPFK VGQSVLKDQN KVRRLKQSGE AFLQDGSCIN VAPHLHKCRE
CRLERYRKSR EQDSDDDDPN VACRFFHFRR LAFTKKGVLR VEGFLSPQQS DSMAMGLWLP
SITIQEGLDL DTSKYILANV GDQFCQLVMS EKEAMMMVEP HQKVAWKRAV RGVREMCDVC
ETTLFNIHWV CRKCGFGVCL DCYRLRKNRP PEVEDGPEEE VFSWLKCAKG QPHEPQNLMP
TQIIPGTALY SIGDMVHAAR GKWGIKANCP CTSRHKTLMR PSAPNGLSQS GAAHSSGNGT
TSTSSTTRPN EESAAGVVVK TEPVEEPTSA DTTSSTSGTN SSTSSPAPAP TSAPTLLPPS
LPPPSLPPPS LPPAPALVPT PPAKDSKSSS SALHWLADLA TQKEPKESLR SMMGRDSRSP
FGLDSFSTLS KPSGSSPKLF NSLLLGAGPS QPKAEGTSLR DLLNSGSGKL PQGPTEGGVP
FPPVFSTASQ ADKMKGGLPN FLDHIIASVV ETKKSEVRRA SGSAEVIESA TAPRREGVMG
LSVLDPHTSH SWLCDGRLLC LQDPSNPNNW KIFRECWKQG QPVLVSGIHR KLKEHLWRPE
AFSEEFGDQD VDLVNCRNCA IISDVKVREF WDGFQVISKR LQGSDGQPMV LKLKDWPPGE
DFRDMMPTRF NDLMDNLPLP EYTKRDGRLN LASRLPNFFV RPDLGPKMYN AYGLISTEDR
KVGTTNLHLD VSDAVNVMVY VGIPEGENDQ ESEADLAGFK EVMQTIEEGD VDDMTKRRVY
EIKEKPGALW HIYAAKDAEK IRELLRKVGE EQGQENPPDH DPIHDQSWYL DQTLRRRLYE
EYGVQGWSIV QFLGDAVFIP AGAPHQVHNL YSCIKAAEDF VSPEHVKHCF RLTQEFRHLS
NTHTNHEDKL QVKNIIYHAV KDAVATLKAH EPKLGRS
//
