KDM5B_CHICK
ID KDM5B_CHICK Reviewed; 1522 AA.
AC Q5F3R2;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Lysine-specific demethylase 5B;
DE EC=1.14.11.67 {ECO:0000250|UniProtKB:Q80Y84};
DE AltName: Full=Histone demethylase JARID1B;
DE AltName: Full=Jumonji/ARID domain-containing protein 1B;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase 5B {ECO:0000305};
GN Name=KDM5B; Synonyms=JARID1B; ORFNames=RCJMB04_9d3;
OS Gallus gallus (Chicken).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
OC Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae;
OC Phasianinae; Gallus.
OX NCBI_TaxID=9031;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=CB; TISSUE=Bursa of Fabricius;
RX PubMed=15642098; DOI=10.1186/gb-2004-6-1-r6;
RA Caldwell R.B., Kierzek A.M., Arakawa H., Bezzubov Y., Zaim J., Fiedler P.,
RA Kutter S., Blagodatski A., Kostovska D., Koter M., Plachy J., Carninci P.,
RA Hayashizaki Y., Buerstedde J.-M.;
RT "Full-length cDNAs from chicken bursal lymphocytes to facilitate gene
RT function analysis.";
RL Genome Biol. 6:R6.1-R6.9(2005).
CC -!- FUNCTION: Histone demethylase that demethylates 'Lys-4' of histone H3,
CC thereby playing a central role in histone code. Does not demethylate
CC histone H3 'Lys-9' or H3 'Lys-27'. Demethylates trimethylated,
CC dimethylated and monomethylated H3 'Lys-4'. Acts as a transcriptional
CC corepressor. May repress the CLOCK-ARNTL/BMAL1 heterodimer-mediated
CC transcriptional activation of the core clock component PER2.
CC {ECO:0000250|UniProtKB:Q80Y84, ECO:0000250|UniProtKB:Q9UGL1}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=3 2-oxoglutarate + N(6),N(6),N(6)-trimethyl-L-lysyl(4)-
CC [histone H3] + 3 O2 = 3 CO2 + 3 formaldehyde + L-lysyl(4)-[histone
CC H3] + 3 succinate; Xref=Rhea:RHEA:60208, Rhea:RHEA-COMP:15537,
CC Rhea:RHEA-COMP:15547, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:61961; EC=1.14.11.67;
CC Evidence={ECO:0000250|UniProtKB:Q80Y84};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00355,
CC ECO:0000255|PROSITE-ProRule:PRU00537}.
CC -!- DOMAIN: Both the JmjC domain and the JmjN domain are required for
CC enzymatic activity (By similarity). However ARID and PHD-type 1 domain
CC are not required for activity per se but contributed to recognition of
CC the H3(1-21)K4me2 substrate peptide (By similarity). {ECO:0000250,
CC ECO:0000250|UniProtKB:Q9UGL1}.
CC -!- DOMAIN: The 2 first PHD-type zinc finger domains are required for
CC transcription repression activity. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; AJ851588; CAH65222.1; -; mRNA.
DR RefSeq; NP_001026200.1; NM_001031029.1.
DR AlphaFoldDB; Q5F3R2; -.
DR BMRB; Q5F3R2; -.
DR SMR; Q5F3R2; -.
DR STRING; 9031.ENSGALP00000000581; -.
DR PaxDb; Q5F3R2; -.
DR PRIDE; Q5F3R2; -.
DR Ensembl; ENSGALT00000071675; ENSGALP00000056668; ENSGALG00000038948.
DR GeneID; 421168; -.
DR KEGG; gga:421168; -.
DR CTD; 10765; -.
DR VEuPathDB; HostDB:geneid_421168; -.
DR eggNOG; KOG1246; Eukaryota.
DR GeneTree; ENSGT00940000157076; -.
DR InParanoid; Q5F3R2; -.
DR OrthoDB; 664180at2759; -.
DR PhylomeDB; Q5F3R2; -.
DR PRO; PR:Q5F3R2; -.
DR Proteomes; UP000000539; Chromosome 26.
DR Bgee; ENSGALG00000038948; Expressed in testis and 12 other tissues.
DR ExpressionAtlas; Q5F3R2; baseline and differential.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0042393; F:histone binding; ISS:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0032453; F:histone H3-methyl-lysine-4 demethylase activity; ISS:UniProtKB.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR GO; GO:0034720; P:histone H3-K4 demethylation; ISS:UniProtKB.
DR GO; GO:0048511; P:rhythmic process; IEA:UniProtKB-KW.
DR Gene3D; 1.10.150.60; -; 1.
DR Gene3D; 3.30.40.10; -; 2.
DR InterPro; IPR001606; ARID_dom.
DR InterPro; IPR036431; ARID_dom_sf.
DR InterPro; IPR003347; JmjC_dom.
DR InterPro; IPR003349; JmjN.
DR InterPro; IPR013637; Lys_sp_deMease-like_dom.
DR InterPro; IPR019786; Zinc_finger_PHD-type_CS.
DR InterPro; IPR004198; Znf_C5HC2.
DR InterPro; IPR011011; Znf_FYVE_PHD.
DR InterPro; IPR001965; Znf_PHD.
DR InterPro; IPR019787; Znf_PHD-finger.
DR InterPro; IPR013083; Znf_RING/FYVE/PHD.
DR Pfam; PF01388; ARID; 1.
DR Pfam; PF02373; JmjC; 1.
DR Pfam; PF02375; JmjN; 1.
DR Pfam; PF00628; PHD; 3.
DR Pfam; PF08429; PLU-1; 1.
DR Pfam; PF02928; zf-C5HC2; 1.
DR SMART; SM00501; BRIGHT; 1.
DR SMART; SM00558; JmjC; 1.
DR SMART; SM00545; JmjN; 1.
DR SMART; SM00249; PHD; 3.
DR SUPFAM; SSF46774; SSF46774; 1.
DR SUPFAM; SSF57903; SSF57903; 3.
DR PROSITE; PS51011; ARID; 1.
DR PROSITE; PS51184; JMJC; 1.
DR PROSITE; PS51183; JMJN; 1.
DR PROSITE; PS01359; ZF_PHD_1; 2.
DR PROSITE; PS50016; ZF_PHD_2; 3.
PE 2: Evidence at transcript level;
KW Biological rhythms; Chromatin regulator; Dioxygenase; Iron; Metal-binding;
KW Nucleus; Oxidoreductase; Reference proteome; Repeat; Repressor;
KW Transcription; Transcription regulation; Zinc; Zinc-finger.
FT CHAIN 1..1522
FT /note="Lysine-specific demethylase 5B"
FT /id="PRO_0000292414"
FT DOMAIN 10..51
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 75..165
FT /note="ARID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00355"
FT DOMAIN 428..594
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 284..334
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 667..719
FT /note="C5HC2"
FT /evidence="ECO:0000250|UniProtKB:Q9UGL1"
FT ZN_FING 1151..1199
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 1462..1516
FT /note="PHD-type 3"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 180..229
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1353..1373
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1400..1460
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 206..229
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1417..1439
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 400
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 474
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 476
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 482
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 484
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 492
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 562
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
SQ SEQUENCE 1522 AA; 173462 MW; 69148B3145D7C010 CRC64;
MAEFLPPPEC PVFEPSWEEF ADPFAFIHKI RPIAEQTGIC KVRPPPDWQP PFACDVDKLH
FTPRIQRLNE LEAQTRVKLN FLDQIAKFWE LQGCTLKIPH VERKILDLFQ LNRLVAEEGG
FDVVCKERKW TKIATRMGFA PGKAVGSHIR AHYERILYPY NLFQSGASLL CLQKPDLTSD
TKDKEYKPHD IPQRQSVQPS ESCPPARRAK RLRAEATNIK TESDSPEVRT HNLRRRMGCA
PPKCENEKET YSAVKLAEKR EHAGEQERDK AKARSKKPTS AVDLYVCLLC GSGNDEDRLL
LCDGCDDSYH TFCLIPPLHD VPKGDWRCPQ CLAQECNKPQ EAFGFEQAAR DYTLRTFGEM
ADAFKSDYFN MPVHMVPTEL VEKEFWRLVS TIEEDVTVEY GADIASKEFG SGFPVRDGKF
KVRPEEEEYL DSGWNLNNMP VMEQSVLAHI TADICGMKLP WLYVGMCFSS FCWHIEDHWS
YSINYLHWGE PKTWYGAPGY AAEQLEDVMK KLAPELFESQ PDLLHQLVTI MNPNTLMAHG
VPVYRTNQCA GEFVITFPRA YHSGFNQGFN FAEAVNFCTV DWLPLGRQCI EHYRLLSRYC
VFSHDEMICK MASKADILDV VVASTVQKDM AIMIDDEKML REKVQKLGVT DSERVAFELF
PDDERQCYKC KTTCFMSAVY CPCKPGLLVC LYHVEDLCSC PTYQYKLGYR YTLEELYPMM
NALKMRAESY NEWASNVNEA LEAKISNKRS LISFKALIEE SELKKFPDND LLRHLRLVTQ
DADKCASVAQ QLLNGKRQTR YRSGGGKCPN QLTVNELRLF VRQLYALPCV LSQTPLLKDL
LDRVEAFQQQ SQKLLSEEMP SAAELQELLD VSFDFDVDLP QLAELRVRLE QARWLEDVQM
ASAEQNSLTL DDMRRLIDSG VGLAPYPAVE KAMAKLQELL TVSEHWDDKA RNLIKARPRQ
SLSSLVVAVK EIEEIPAYLP SGAALKDAVQ KAQDWLQEVE ALQVGGRVPV LDTLVELVTR
GRSIPVHLDY LPRLESLVAE VQAWKECAAN TFLCENSPYS LLEVLCPRCD IGTLGLKRKQ
KKLKEPMPSG KKRSTKLESL SDLERALSES KDTASAMATL GEARLKEMEA LRSLRAANEG
KVLCSEEDAE LKVCVCQKEP AAPMIQCELC RGFFHTGCVS VPHALQGPRV WLCPQCRRSE
KPPLEKILPL LASLQRIRVR LPEGDALRYM IERTVNWQHR AQQMLYSGNL KLLQDKVGSG
LLYNRWQSTA GPLPETNKVS QTIGAMSFSM PHDWDNRTIY LHSPFSTGQQ CIPLHVVSTE
LDELMMEAQL LQVSLPEIQE LYQILFTKQS PSLQAEQKPS VGPSNEKSEC CRGKKDGMSY
MERKLKRRFE RESFCDEKRA RVRKMRTPKK KKLKLSHTKD VSSSSRMERE RERLLEAQRS
SESHLVPSDT SFSEQEDSED EDAICPAVTC LQPEGEEVDW VQCDGSCNQW FHQVCVGISP
EMAEKEDYIC ASCAGKGSPY RK
