KDM5D_CANLF
ID KDM5D_CANLF Reviewed; 1545 AA.
AC Q30DN6;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=Lysine-specific demethylase 5D;
DE EC=1.14.11.67 {ECO:0000250|UniProtKB:Q9BY66};
DE AltName: Full=Histone demethylase JARID1D;
DE AltName: Full=Jumonji/ARID domain-containing protein 1D;
DE AltName: Full=Protein SmcY;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase 5D {ECO:0000305};
GN Name=KDM5D; Synonyms=JARID1D, SMCY;
OS Canis lupus familiaris (Dog) (Canis familiaris).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Carnivora; Caniformia; Canidae; Canis.
OX NCBI_TaxID=9615;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Graves S.S., Venkataraman G.M., Harkey M.A., Gass J., Sangiolo D.,
RA Stone B., Storb R.;
RL Submitted (AUG-2005) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Histone demethylase that specifically demethylates 'Lys-4' of
CC histone H3, thereby playing a central role in histone code. Does not
CC demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79'
CC or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not
CC monomethylated H3 'Lys-4'. May play a role in spermatogenesis. Involved
CC in transcriptional repression of diverse metastasis-associated genes;
CC in this function seems to cooperate with ZMYND8. Suppresses prostate
CC cancer cell invasion. Regulates androgen receptor (AR) transcriptional
CC activity by demethylating H3K4me3 active transcription marks (By
CC similarity). {ECO:0000250|UniProtKB:Q9BY66}.
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:Q9BY66};
CC -!- COFACTOR:
CC Name=L-ascorbate; Xref=ChEBI:CHEBI:38290;
CC Evidence={ECO:0000250|UniProtKB:Q9BY66};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q9BY66};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q9BY66};
CC -!- SUBUNIT: Interacts withPCGF6, MSH5, ZMYND8, AR.
CC {ECO:0000250|UniProtKB:Q9BY66}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q9BY66,
CC ECO:0000255|PROSITE-ProRule:PRU00355, ECO:0000255|PROSITE-
CC ProRule:PRU00537}.
CC -!- DOMAIN: The JmjC domain is required for enzymatic activity.
CC {ECO:0000250|UniProtKB:Q9BY66}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; DQ156494; ABA40834.1; -; mRNA.
DR RefSeq; NP_001106929.1; NM_001113458.1.
DR AlphaFoldDB; Q30DN6; -.
DR SMR; Q30DN6; -.
DR GeneID; 100134936; -.
DR CTD; 8284; -.
DR InParanoid; Q30DN6; -.
DR Proteomes; UP000002254; Unplaced.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0032452; F:histone demethylase activity; IBA:GO_Central.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006338; P:chromatin remodeling; IBA:GO_Central.
DR Gene3D; 1.10.150.60; -; 1.
DR Gene3D; 3.30.40.10; -; 1.
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; 1.
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; 2.
DR SUPFAM; SSF46774; SSF46774; 1.
DR SUPFAM; SSF57903; SSF57903; 2.
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; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Dioxygenase; Iron; Isopeptide bond; Metal-binding;
KW Nucleus; Oxidoreductase; Phosphoprotein; Reference proteome; Repeat;
KW Ubl conjugation; Zinc; Zinc-finger.
FT CHAIN 1..1545
FT /note="Lysine-specific demethylase 5D"
FT /id="PRO_0000292418"
FT DOMAIN 14..55
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 79..169
FT /note="ARID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00355"
FT DOMAIN 461..627
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 317..367
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 700..752
FT /note="C5HC2"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT ZN_FING 1177..1242
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 185..228
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1433..1496
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 198..212
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 214..228
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1465..1482
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 433
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 507
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 509
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 515
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 517
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 525
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 595
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT MOD_RES 295
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 310
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 883
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41230"
FT MOD_RES 887
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 1350
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 229
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 244
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 274
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
SQ SEQUENCE 1545 AA; 175621 MW; 9867380570721EF2 CRC64;
MESGSDDFLP PPECPVFEPT WAEFRDPLDY ITKIRPIAEK SGICKIRPPA DWQPPFAVEV
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERRIL DLYSLSKIVM
EEGGYEAICK DRRWARVAQR LNYPAGKNIG SLLRSHYERI IYPYEMFQSG ANLVQCNTYP
FDNEEKDKEY KPHGIPLRQS VQPSTFSSYS RRAKRLQPDP EPTEEDIEKN PELKKLQIYG
AGPKMMGLGL MAKDKTLRKK DKEGVLCPRA VLMKEEPRED ERVMSSLPRE DLSHSVEPCT
KMTMQLRTHS SAQFIDLYVC RICSRGDEDD KLLLCDGCDD TYHIFCLIPP LPEIPRGVWR
CPKCIMAECK RPPEAFGFEQ ATQEYTLQSF GEMADSFKAD YFSMPVHMVP TELVEKEFWR
LVSSIEEDVT VEYGADIHSK EFGSGFPVSS SQRILSPEEE EYATSGWNLN VMPVLDQSVL
CHINADISGM KVPWLYVGMV FSAFCWHIED HWSYSINYLH WGEPKTWYGV PSLAAEQLEE
VMKRLTPELF DSQPDLLHQL VTLMNPNTLM SHGVPVVRTN QCAGEFVITF PRAYHSGFNQ
GYNFAEAVNF CTADWLPAGR QCIEHYRRLR RYCVFSHEEL ICKMAAFPEK LDLNLAVAVH
KEMFIMVQEE RRLRKALLEK GITEAEREAF ELLPDDERQC IKCKTTCFLS ALACYDCPDG
LVCLSHINDL CKCSSSRQYL RYRYTLDELP AMLHKLKIRA ESFDTWANKV RVALEVEDGR
KRSFEELRAL ESEARERRFP NSELLQRLRN CMHEAEACVS QVLGLVSGQE ARIQTSPLTL
TELRVLLEQM SSLPCAMHQI EDVKEVLEQV EAYQIEAREA LASLCPSVGL MRSLLEKGQQ
LGVDVPEAHQ LQQQVEQARW LDDVKKALAP SAQRGSLVIM QGLLVTGTKI ASSPCVDKAR
AELQELLTIA ERWEEKAHFC LEARQKHPPA TLEAIIREAE NIPVHLPNIQ ALKDALAKAQ
AWIADVDEIQ NGDHYPCLDD LECLVAVGRD LPVSLEELRQ LELQVLTAHS WREKASRMFL
KKNSCYTLLE VLCPCAHAGS DSSKRRRWIE KELRLYRSCT DTELLGLSAQ DLRDPGSVIV
AFKEGEQKEK EGILQLRRTN SAKPSPLASS TTASSATSIC VCGKVPAGVG TLQCDLCQDW
FHGQCVSVPH ILSSSRPSPT SSPLLAWWEW DTKFLCPLCM RSRRPRLETI LALLVALQRL
PVRLPEGEAL QCLTERAIVW QGRARQALAS KDVTTLLGQL AELRHQLQAE TRLQEPYHST
PACAPLREGS GRDMPKQVPG LLPNVDSTSS HEKIASVQGS DLEVLSSLLS QLSGPVLDLP
EATRVPLEEL MLEGDLLEVT LDENHRIWQL LQAGQPPDLE RICTLLELEK PEHKGSRTRG
RALEKRRRRQ QQEVDLGMKS KNLVQEELQS KKARNSGNKS EEGQEEEEFE EERDSENIFL
TCSVDHSSVL KVNPNSVRQN DSGITASFPS LTPLLHQPYP QQDIL
