KDM5C_PIG
ID KDM5C_PIG Reviewed; 1516 AA.
AC A1YVX4;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=Lysine-specific demethylase 5C;
DE EC=1.14.11.67 {ECO:0000250|UniProtKB:P41229};
DE AltName: Full=Histone demethylase JARID1C;
DE AltName: Full=Jumonji/ARID domain-containing protein 1C;
DE AltName: Full=Protein SmcX;
DE AltName: Full=[histone H3]-trimethyl-L-lysine(4) demethylase 5C {ECO:0000305};
GN Name=KDM5C; Synonyms=JARID1C, SMCX;
OS Sus scrofa (Pig).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Suina; Suidae; Sus.
OX NCBI_TaxID=9823;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Yi L., Xu Y.;
RL Submitted (NOV-2006) 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'. Participates in transcriptional repression
CC of neuronal genes by recruiting histone deacetylases and REST at
CC neuron-restrictive silencer elements (By similarity).
CC {ECO:0000250|UniProtKB:P41229}.
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:P41229};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:P41229};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:P41229};
CC -!- SUBUNIT: Part of two distinct complexes, one containing E2F6, and the
CC other containing REST. {ECO:0000250|UniProtKB:P41229}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00355,
CC ECO:0000255|PROSITE-ProRule:PRU00537}.
CC -!- DOMAIN: The first PHD-type zinc finger domain recognizes and binds H3-
CC K9Me3. {ECO:0000250}.
CC -!- DOMAIN: Both the JmjC domain and the JmjN domain are required for
CC enzymatic activity. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the JARID1 histone demethylase family.
CC {ECO:0000305}.
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DR EMBL; EF139241; ABL74503.1; -; mRNA.
DR RefSeq; NP_001090902.1; NM_001097433.1.
DR AlphaFoldDB; A1YVX4; -.
DR BMRB; A1YVX4; -.
DR SMR; A1YVX4; -.
DR STRING; 9823.ENSSSCP00000013112; -.
DR PaxDb; A1YVX4; -.
DR GeneID; 100037295; -.
DR KEGG; ssc:100037295; -.
DR CTD; 8242; -.
DR eggNOG; KOG1246; Eukaryota.
DR InParanoid; A1YVX4; -.
DR OrthoDB; 664180at2759; -.
DR BRENDA; 1.14.11.67; 6170.
DR Proteomes; UP000008227; Unplaced.
DR Proteomes; UP000314985; Unplaced.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0034647; F:histone H3-tri/di/monomethyl-lysine-4 demethylase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
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 Transcription; Transcription regulation; Ubl conjugation; Zinc;
KW Zinc-finger.
FT CHAIN 1..1516
FT /note="Lysine-specific demethylase 5C"
FT /id="PRO_0000292417"
FT DOMAIN 14..55
FT /note="JmjN"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00537"
FT DOMAIN 24..128
FT /note="ARID"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00355"
FT DOMAIN 427..593
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT ZN_FING 283..333
FT /note="PHD-type 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT ZN_FING 666..718
FT /note="C5HC2"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT ZN_FING 1144..1209
FT /note="PHD-type 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00146"
FT REGION 142..186
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 216..262
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1274..1305
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1400..1516
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 171..186
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 248..262
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1417..1446
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1471..1516
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 399
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 473
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 475
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 481
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 483
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 491
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:P29375"
FT BINDING 561
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT MOD_RES 246
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 260
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 276
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 852
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41230"
FT MOD_RES 856
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT MOD_RES 1318
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 164
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 188
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 203
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 233
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 254
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
FT CROSSLNK 1086
FT /note="Glycyl lysine isopeptide (Lys-Gly) (interchain with
FT G-Cter in SUMO2)"
FT /evidence="ECO:0000250|UniProtKB:P41229"
SQ SEQUENCE 1516 AA; 170584 MW; 8DE6C52868E3E7E3 CRC64;
MEPGSDDFLP PPECPVFEPS WAEFRDPLGY IAKIRPIAEK SGICKIRPPA DWQPPFAVEV
DNFRFTPRIQ RLNELEIVVE EGGYEAICKD RRWARVAQRL NYPPGKNIGS LLRSHYERIV
YPYEMYQSGA NLVQCNTRPF DNEEKDKEYK PHSIPLRQSV QPSKFNSYGR RAKRLQPDPE
PTEEDIEKNP ELKKLQIYGA GPKMMGLGLM AKDKTLRKKD KEGPECPPTV VVKEESGGDV
KVESTSPKTF LESKEELSHS PEPCTKMTMR LRRNHSNAQF IESYVCRMCS RGDEDDKLLL
CDGCDDNYHI FCLLPPLPEI PKGVWRCPKC VMAECKRPPE AFGFEQATRE YTLQSFGEMA
DSFKADYSNM PVHMVPTELV EKEFWRLVNS IEEDVTVEYG ADIHSKEFGS GFPVSDSKRH
LTPEEEEYAT SGWNLNVMPV LEQSVLCHIN ADISGMKVPW LYVGMVFSAF CWHIEDHWSY
SINYLHWGEP KTWYGVPSLA AEHLEEVMKK LTPELFDSQP DLLHQLVTLM NPNTLMSHGV
PVVRTNQCAG EFVITFPRAY HSGFNQGYNF AEAVNFCTAD WLPAGRQCIE HYRRLRRYCV
FSHEELICKM AACPEKLDLN LAAAVHKEMF IMVQEERRLR KALLEKGITE AEREAFELLP
DDERQCIKCK TTCFLSALAC YDCPDGLVCL SHINDLCKCS SSRQYLRYRY TLDELPAMLH
KLKVRAESFD TWANKVRVAL EVEDGRKRSL EELRALESEA RERRFPNSEL LQRLKNCLSE
AEACVSRALG LVSGQEAGPH RVAGLQMTLA ELRAFLDQMN NLPCAMHQIG DVKGILEQVE
AYQAEAREAL ASLPSSPGLL QSLLERGRQL GVEVPEAQQL QRQVEQARWL DEVKRTLAPS
ARRGTLAVMR GLLVAGASVA PSPAVDKAQA ELQELLTIAE RWEEKAHLCL EARQKHPPAT
LEAIIHEAEN IPVHLPNIQA LKEALAKARA WIADVDEIQN GDHYPCLDDL EGLVAVGRDL
PVGLEELRQL ELQVLTAHSW REKASKTFLK KNSCYTLLEV LCPCADAGSD STKRSRWMEK
ELGLYKSDTE LLGLSAQDLR DPGSVIVAFK EGEQKEKEGI LQLRRTNSAK PSPLASPNTS
SSATSICVCG QVPAGVGALQ CDLCQDWFHG RCVSVPRLLS SPRPSPTSSP LLAWWEWDTK
FLCPLCMRSR RPRLETILAL LVALQRLPVR LPEGEALQCL TERAISWQGR ARQALAFEDV
TALLGRLAEL RQRLQAEPRP EEPPTYPSTP AFDPLREGSG KDMPKVQGLL ENGDSVTSPE
KVAPGEGSDL ELLSSLLPQL TGPVLELPEA TRAPLEELML EGDLLEVTLD ENHSIWQLLQ
AGKPPDLARI RTLLELEKAE RHGSRARGRA LERRRRRKVD RGGEGDDPAR EELEPKRVRS
SWPEAEEAHE EEELEEETGG EGPPQPLPAT GSPSTQENQN GLEPALGASS GSSVPFSTLT
PRLHMSCPQQ PPQQQL
