ID JMJD4_HUMAN Reviewed; 417 AA.
AC Q9H9V9; A0A087WT84; Q5TBZ1; Q5TBZ6; Q9H970;
DT 26-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 24-JAN-2024, sequence version 3.
DT 27-MAR-2024, entry version 150.
DE RecName: Full=2-oxoglutarate and iron-dependent oxygenase JMJD4 {ECO:0000303|PubMed:24486019};
DE EC=1.14.11.- {ECO:0000269|PubMed:24486019};
DE AltName: Full=JmjC domain-containing protein 4;
DE AltName: Full=Jumonji domain-containing protein 4;
DE AltName: Full=Lysyl-hydroxylase JMJD4 {ECO:0000303|PubMed:24486019};
GN Name=JMJD4;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3), AND VARIANT
RP VAL-11 (ISOFORM 1).
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16710414; DOI=10.1038/nature04727;
RA Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A.,
RA Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C.,
RA Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K.,
RA Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C.,
RA Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W.,
RA Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J.,
RA Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J.,
RA Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y.,
RA Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J.,
RA Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H.,
RA Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L.,
RA Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J.,
RA Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S.,
RA Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K.,
RA Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R.,
RA Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M.,
RA Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S.,
RA Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J.,
RA Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W.,
RA McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N.,
RA Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V.,
RA Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J.,
RA Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E.,
RA Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S.,
RA Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M.,
RA White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H.,
RA Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E.,
RA Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G.,
RA Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.;
RT "The DNA sequence and biological annotation of human chromosome 1.";
RL Nature 441:315-321(2006).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH ETF1 AND ETF1-GSPT1 COMPLEX,
RP COFACTOR, SUBCELLULAR LOCATION, AND MUTAGENESIS OF HIS-189.
RX PubMed=24486019; DOI=10.1016/j.molcel.2013.12.028;
RA Feng T., Yamamoto A., Wilkins S.E., Sokolova E., Yates L.A., Muenzel M.,
RA Singh P., Hopkinson R.J., Fischer R., Cockman M.E., Shelley J.,
RA Trudgian D.C., Schoedel J., McCullagh J.S., Ge W., Kessler B.M.,
RA Gilbert R.J., Frolova L.Y., Alkalaeva E., Ratcliffe P.J., Schofield C.J.,
RA Coleman M.L.;
RT "Optimal translational termination requires C4 lysyl hydroxylation of
RT eRF1.";
RL Mol. Cell 53:645-654(2014).
CC -!- FUNCTION: Catalyzes the 2-oxoglutarate and iron-dependent C4-lysyl
CC hydroxylation of ETF1 at 'Lys-63' thereby promoting the translational
CC termination efficiency of ETF1. {ECO:0000269|PubMed:24486019}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + L-lysyl-[protein] + O2 = 4-hydroxy-L-lysyl-
CC [protein] + CO2 + succinate; Xref=Rhea:RHEA:57156, Rhea:RHEA-
CC COMP:9752, Rhea:RHEA-COMP:15084, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:141495;
CC Evidence={ECO:0000269|PubMed:24486019};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000269|PubMed:24486019};
CC -!- SUBUNIT: Interacts with ETF1 (PubMed:24486019). Interacts with the
CC ETF1-GSPT1 complex (PubMed:24486019). {ECO:0000269|PubMed:24486019}.
CC -!- INTERACTION:
CC Q9H9V9; P62805: H4C9; NbExp=3; IntAct=EBI-2866290, EBI-302023;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:24486019}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing, Alternative initiation; Named isoforms=3;
CC Name=3;
CC IsoId=Q9H9V9-3; Sequence=Displayed;
CC Name=1;
CC IsoId=Q9H9V9-1; Sequence=VSP_062164;
CC Name=2;
CC IsoId=Q9H9V9-2; Sequence=VSP_062165;
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DR EMBL; AK022579; BAB14109.1; -; mRNA.
DR EMBL; AK023030; BAB14366.1; -; mRNA.
DR EMBL; AL136378; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001154937.1; NM_001161465.1. [Q9H9V9-2]
DR RefSeq; NP_075383.2; NM_023007.2. [Q9H9V9-3]
DR AlphaFoldDB; Q9H9V9; -.
DR SMR; Q9H9V9; -.
DR BioGRID; 122393; 63.
DR IntAct; Q9H9V9; 43.
DR MINT; Q9H9V9; -.
DR STRING; 9606.ENSP00000355720; -.
DR iPTMnet; Q9H9V9; -.
DR PhosphoSitePlus; Q9H9V9; -.
DR BioMuta; JMJD4; -.
DR DMDM; 150383500; -.
DR EPD; Q9H9V9; -.
DR jPOST; Q9H9V9; -.
DR MassIVE; Q9H9V9; -.
DR MaxQB; Q9H9V9; -.
DR PaxDb; 9606-ENSP00000355720; -.
DR PeptideAtlas; Q9H9V9; -.
DR ProteomicsDB; 81365; -. [Q9H9V9-1]
DR ProteomicsDB; 81366; -. [Q9H9V9-2]
DR Pumba; Q9H9V9; -.
DR Antibodypedia; 20772; 318 antibodies from 30 providers.
DR DNASU; 65094; -.
DR Ensembl; ENST00000438896.3; ENSP00000387830.3; ENSG00000081692.13. [Q9H9V9-2]
DR Ensembl; ENST00000620518.5; ENSP00000477669.1; ENSG00000081692.13. [Q9H9V9-3]
DR GeneID; 65094; -.
DR KEGG; hsa:65094; -.
DR MANE-Select; ENST00000620518.5; ENSP00000477669.1; NM_023007.3; NP_075383.3.
DR UCSC; uc001hrb.3; human. [Q9H9V9-3]
DR AGR; HGNC:25724; -.
DR CTD; 65094; -.
DR DisGeNET; 65094; -.
DR GeneCards; JMJD4; -.
DR HGNC; HGNC:25724; JMJD4.
DR HPA; ENSG00000081692; Low tissue specificity.
DR neXtProt; NX_Q9H9V9; -.
DR OpenTargets; ENSG00000081692; -.
DR PharmGKB; PA142671643; -.
DR VEuPathDB; HostDB:ENSG00000081692; -.
DR eggNOG; KOG2131; Eukaryota.
DR GeneTree; ENSGT00940000159380; -.
DR HOGENOM; CLU_016785_2_2_1; -.
DR InParanoid; Q9H9V9; -.
DR OMA; MFSRRFT; -.
DR OrthoDB; 5346565at2759; -.
DR PhylomeDB; Q9H9V9; -.
DR TreeFam; TF105936; -.
DR PathwayCommons; Q9H9V9; -.
DR Reactome; R-HSA-9629569; Protein hydroxylation.
DR SignaLink; Q9H9V9; -.
DR BioGRID-ORCS; 65094; 12 hits in 1159 CRISPR screens.
DR ChiTaRS; JMJD4; human.
DR GenomeRNAi; 65094; -.
DR Pharos; Q9H9V9; Tbio.
DR PRO; PR:Q9H9V9; -.
DR Proteomes; UP000005640; Chromosome 1.
DR RNAct; Q9H9V9; Protein.
DR Bgee; ENSG00000081692; Expressed in left adrenal gland cortex and 106 other cell types or tissues.
DR ExpressionAtlas; Q9H9V9; baseline and differential.
DR Genevisible; Q9H9V9; HS.
DR GO; GO:0005737; C:cytoplasm; IDA:UniProtKB.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0016706; F:2-oxoglutarate-dependent dioxygenase activity; IMP:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0106156; F:peptidyl-lysine 4-dioxygenase activity; EXP:Reactome.
DR GO; GO:0043565; F:sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0045905; P:positive regulation of translational termination; IMP:UniProtKB.
DR GO; GO:0018126; P:protein hydroxylation; IMP:UniProtKB.
DR Gene3D; 2.60.120.650; Cupin; 1.
DR InterPro; IPR003347; JmjC_dom.
DR PANTHER; PTHR12480:SF6; 2-OXOGLUTARATE AND IRON-DEPENDENT OXYGENASE JMJD4; 1.
DR PANTHER; PTHR12480; ARGININE DEMETHYLASE AND LYSYL-HYDROXYLASE JMJD; 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 Alternative initiation; Alternative splicing; Cytoplasm; Dioxygenase; Iron;
KW Metal-binding; Oxidoreductase; Reference proteome.
FT CHAIN 1..417
FT /note="2-oxoglutarate and iron-dependent oxygenase JMJD4"
FT /id="PRO_0000291959"
FT DOMAIN 142..301
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 189
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT BINDING 191
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT BINDING 269
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT VAR_SEQ 1
FT /note="M -> MRAGPEPQALAGQKRGALRLLVPRLVLTVSAPAEVRRRVLRPVLSWM
FT (in isoform 1)"
FT /id="VSP_062164"
FT VAR_SEQ 308..323
FT /note="Missing (in isoform 2)"
FT /id="VSP_062165"
FT VARIANT 19
FT /note="D -> E (in dbSNP:rs2295994)"
FT /id="VAR_032900"
FT VARIANT 415
FT /note="A -> V (in dbSNP:rs3087908)"
FT /id="VAR_032901"
FT MUTAGEN 189
FT /note="H->A: Loss of interaction with ETF1 and its ability
FT to hydroxylate ETF1."
FT /evidence="ECO:0000269|PubMed:24486019"
FT CONFLICT 198
FT /note="W -> R (in Ref. 1; BAB14366)"
FT /evidence="ECO:0000305"
FT CONFLICT 399
FT /note="Q -> R (in Ref. 1; BAB14366)"
FT /evidence="ECO:0000305"
FT VARIANT Q9H9V9-1:11
FT /note="A -> V (in dbSNP:rs7419238)"
FT /evidence="ECO:0000269|PubMed:14702039"
FT /id="VAR_088561"
SQ SEQUENCE 417 AA; 47425 MW; 371B260A06ABD566 CRC64;
MDRETRALAD SHFRGLGVDV PGVGQAPGRV AFVSEPGAFS YADFVRGFLL PNLPCVFSSA
FTQGWGSRRR WVTPAGRPDF DHLLRTYGDV VVPVANCGVQ EYNSNPKEHM TLRDYITYWK
EYIQAGYSSP RGCLYLKDWH LCRDFPVEDV FTLPVYFSSD WLNEFWDALD VDDYRFVYAG
PAGSWSPFHA DIFRSFSWSV NVCGRKKWLL FPPGQEEALR DRHGNLPYDV TSPALCDTHL
HPRNQLAGPP LEITQEAGEM VFVPSGWHHQ VHNLDDTISI NHNWVNGFNL ANMWRFLQQE
LCAVQEEVSE WRDSMPDWHH HCQVIMRSCS GINFEEFYHF LKVIAEKRLL VLREAAAEDG
AGLGFEQAAF DVGRITEVLA SLVAHPDFQR VDTSAFSPQP KELLQQLREA VDAAAAP
//
