KDM5D_PANTR
ID KDM5D_PANTR Reviewed; 1535 AA.
AC Q5XUN4;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 93.
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 Pan troglodytes (Chimpanzee).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Pan.
OX NCBI_TaxID=9598;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Hughes J.F., Pyntikova T., Skaletsky H., Minx P.J., Rozen S., Wilson R.K.,
RA Page D.C.;
RT "The DNA sequence of the chimpanzee Y chromosome.";
RL Submitted (JUL-2004) 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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AY736376; AAU82116.1; -; mRNA.
DR RefSeq; NP_001008975.1; NM_001008975.1.
DR AlphaFoldDB; Q5XUN4; -.
DR BMRB; Q5XUN4; -.
DR SMR; Q5XUN4; -.
DR STRING; 9598.ENSPTRP00000038793; -.
DR PaxDb; Q5XUN4; -.
DR PRIDE; Q5XUN4; -.
DR GeneID; 449032; -.
DR KEGG; ptr:449032; -.
DR CTD; 8284; -.
DR eggNOG; KOG1246; Eukaryota.
DR InParanoid; Q5XUN4; -.
DR OrthoDB; 664180at2759; -.
DR Proteomes; UP000002277; 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 GO; GO:0070076; P:histone lysine demethylation; IEA:UniProt.
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; 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..1535
FT /note="Lysine-specific demethylase 5D"
FT /id="PRO_0000200590"
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 458..624
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 314..364
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 697..749
FT /note="C5HC2"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT ZN_FING 1174..1235
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 192..227
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1425..1519
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 197..211
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 212..227
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1447..1467
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1474..1489
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1490..1519
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 430
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 504
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 506
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 512
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 514
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 522
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 592
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT MOD_RES 291
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 307
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 884
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 1342
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 205
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
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 272
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
SQ SEQUENCE 1535 AA; 173743 MW; D1C6E59F8A02C435 CRC64;
MEPGCNEFLP PPECPVFEPS WAEFQDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
DNFRFTPRIQ RLNELEAQTR VKLNYLDQIA KFWEIQGSSL KIPNVERKIL DLYSLSKIVI
EEGGYEAICK DRRWARVAQR LHYPPGKNIG SLLRSHYERI IYPYEMFQSG ANHVQCNTHP
FDNEVKDKEY KPHSIPLRQS VQPSKFSSYS RRAKRLQPDP EPTEEDIEKN PELKKLQIYG
PGPKMMGLGL MAKDKDKTVH KKVTCPPTVT VKDEQSGGGN VSSTLLKQHL SLEPCTKTTM
QLRKNHSSAQ FIDSYICQVC SRGDEDDKLL FCDGCDDNYH IFCLLPPLPE IPRGIWRCPK
CILAECKQPP EAFGFEQATQ EYTLQSFGEM ADSFKSDYFN MPVHMVPTEL LEKEFWRLVS
SIEEDVTVEY GADIHYKEFG SGFPVSNSKQ NLSPEEKEYA TSGWNLNVMP VLAQSVLCHI
NADISGMKVP WLYVGMVFSA FCWHIEDHWS YSINYLHWGE PKTWYGVPSL AAEHLEEVMK
MLTPELFDSQ PDLLHQLVTL MNPNTLMSHG VPVVRTNQCA GEFVITFPRA YHSGFNQGYN
FAEAVNFCTA DWLPAGRQCI EHYRRLRRYC VFSHEELICK MAAFPETLDL NLAVAVHKEM
FIMVQEERRL RKALLEKGVT EAEREAFELL PDDERQCIKC KTTCFLSALA CYDCPDGLVC
LSHINDLCKC SSSRQYLRYR YTLDELPTML HKLKIRAESF DTWANKVRVA LEVEDGRKRS
FEELRALESE ARERRFPNSE LLQRLKNCLS EVEACIAQVL GLVSGQVARM DTPQLTLTEL
RVLLEQMGSL PCAMHQIGDV KDVLEQVEAY QDEAREALAT LPSSPGLLRS LLERGQQLGV
EVPEAHQLQQ QVEQAQWLDE VKQALAPSAH RGSLVIMQGL LVMGAKIASS PSVDKARAEL
QELLTIAERW EEKAHFCLEA RQKHPPATLE AIIRETENIP VHLPNIQALK EALTKAQAWI
ADVDEIQNGD HYPCLDDLEG LVAVGRDLPV GLEELRQLEL QVLTAHSWRE KASKTFLKKN
SCYTLLEVLC PCADAGSDST KRSRWMEKAL GLYQCDTELL GLSAQDLRDP GSLIVAFKEG
EQKEKEGILQ LRRTNSAKPS PLAPSLMASS PTSICVCGQV PAGVGALQCD LCQDWFHGQC
VSVPHLLTSP KPSLTSSPLL AWWEWDTKFL CPLCMRSRRP RLETILALLV ALQRLPVRLP
EGEALQCLTE RAIGWQDRAR KALASEDVTA LLRHLAELRQ QLQAKPRPVY TSATACDPIR
EGSGNNISKV QGLLENGDSV ISPENMAPGK GSDLELLSSL LPQLTGPVLE LPEAIRAPLE
ELMMEGDLLE VTLDENHSIW QLLQAGQPPD LDRIRTLLEL EKFEHQGSRT RSRALERRRR
QQKVDQGRNV ENLVQQELQS KRARSSGIMS QVGREEEHYQ EKADRENMFL TPSTDHSPSL
KGNQNSLQHK DSGSSAACPS LMPWLQLSYS DEQQL
