JMJD6_CHICK
ID JMJD6_CHICK Reviewed; 414 AA.
AC Q5ZMK5;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 84.
DE RecName: Full=Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6;
DE EC=1.14.11.-;
DE AltName: Full=Histone arginine demethylase JMJD6;
DE AltName: Full=JmjC domain-containing protein 6;
DE AltName: Full=Jumonji domain-containing protein 6;
DE AltName: Full=Lysyl-hydroxylase JMJD6;
DE AltName: Full=Peptide-lysine 5-dioxygenase JMJD6;
DE AltName: Full=Phosphatidylserine receptor;
DE Short=Protein PTDSR;
GN Name=JMJD6; Synonyms=PTDSR; ORFNames=RCJMB04_1m8;
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: Dioxygenase that can both act as a arginine demethylase and a
CC lysyl-hydroxylase. Acts as a lysyl-hydroxylase that catalyzes 5-
CC hydroxylation on specific lysine residues of target proteins such as
CC U2AF2/U2AF65 and LUC7L2. Regulates RNA splicing by mediating 5-
CC hydroxylation of U2AF2/U2AF65, affecting the pre-mRNA splicing activity
CC of U2AF2/U2AF65. Hydroxylates its own N-terminus, which is required for
CC homooligomerization. In addition to peptidyl-lysine 5-dioxygenase
CC activity, may act as an RNA hydroxylase, as suggested by its ability to
CC bind single strand RNA. Also acts as an arginine demethylase which
CC preferentially demethylates asymmetric dimethylation. Demethylates
CC histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me),
CC including mono-, symmetric di- and asymmetric dimethylated forms,
CC thereby playing a role in histone code. However, histone arginine
CC demethylation may not constitute the primary activity in vivo. In
CC collaboration with BRD4, interacts with the positive transcription
CC elongation factor b (P-TEFb) complex in its active form to regulate
CC polymerase II promoter-proximal pause release for transcriptional
CC activation of a large cohort of genes. Demethylates other arginine
CC methylated-proteins such as ESR1. Has no histone lysine demethylase
CC activity (By similarity). Required for differentiation of multiple
CC organs during embryogenesis. Acts as a key regulator of hematopoietic
CC differentiation (By similarity). {ECO:0000250|UniProtKB:Q6NYC1,
CC ECO:0000250|UniProtKB:Q9ERI5}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + L-lysyl-[protein] + O2 = (5S)-5-hydroxy-L-
CC lysyl-[protein] + CO2 + succinate; Xref=Rhea:RHEA:58360, Rhea:RHEA-
CC COMP:9752, Rhea:RHEA-COMP:15144, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:16810, ChEBI:CHEBI:29969,
CC ChEBI:CHEBI:30031, ChEBI:CHEBI:141843;
CC Evidence={ECO:0000250|UniProtKB:Q6NYC1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 2-oxoglutarate + N(omega),N(omega)'-dimethyl-L-arginyl-
CC [protein] + 2 O2 = 2 CO2 + 2 formaldehyde + L-arginyl-[protein] + 2
CC succinate; Xref=Rhea:RHEA:58348, Rhea:RHEA-COMP:10532, Rhea:RHEA-
CC COMP:11992, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526, ChEBI:CHEBI:16810,
CC ChEBI:CHEBI:16842, ChEBI:CHEBI:29965, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:88221; Evidence={ECO:0000250|UniProtKB:Q6NYC1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + N(omega),N(omega)'-dimethyl-L-arginyl-
CC [protein] + O2 = CO2 + formaldehyde + N(omega)-methyl-L-arginyl-
CC [protein] + succinate; Xref=Rhea:RHEA:58472, Rhea:RHEA-COMP:11990,
CC Rhea:RHEA-COMP:11992, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:65280, ChEBI:CHEBI:88221;
CC Evidence={ECO:0000250|UniProtKB:Q6NYC1};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-oxoglutarate + a 5'-end methyltriphosphate-guanosine-
CC ribonucleotide-snRNA + O2 = a 5'-end triphospho-guanosine-
CC ribonucleotide-snRNA + CO2 + formaldehyde + H(+) + succinate;
CC Xref=Rhea:RHEA:58784, Rhea:RHEA-COMP:15220, Rhea:RHEA-COMP:15221,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:16526,
CC ChEBI:CHEBI:16810, ChEBI:CHEBI:16842, ChEBI:CHEBI:30031,
CC ChEBI:CHEBI:138278, ChEBI:CHEBI:142789;
CC Evidence={ECO:0000250|UniProtKB:Q6NYC1};
CC -!- COFACTOR:
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q6NYC1};
CC Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250|UniProtKB:Q6NYC1};
CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC {ECO:0000250|UniProtKB:Q6NYC1}. Nucleus, nucleolus
CC {ECO:0000250|UniProtKB:Q6NYC1}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q6NYC1}. Note=Mainly found throughout the
CC nucleoplasm outside of regions containing heterochromatic DNA, with
CC some localization in nucleolus. During mitosis, excluded from the
CC nucleus and reappears in the telophase of the cell cycle.
CC {ECO:0000250|UniProtKB:Q6NYC1}.
CC -!- DOMAIN: The nuclear localization signal motifs are necessary and
CC sufficient to target it into the nucleus.
CC {ECO:0000250|UniProtKB:Q6NYC1}.
CC -!- PTM: Hydroxylates its own N-terminus; hydroxylation is required for
CC homooligomerization. {ECO:0000250|UniProtKB:Q6NYC1}.
CC -!- SIMILARITY: Belongs to the JMJD6 family. {ECO:0000305}.
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DR EMBL; AJ719379; CAG31038.1; -; mRNA.
DR RefSeq; NP_001025874.1; NM_001030703.1.
DR AlphaFoldDB; Q5ZMK5; -.
DR SMR; Q5ZMK5; -.
DR STRING; 9031.ENSGALP00000002781; -.
DR PaxDb; Q5ZMK5; -.
DR GeneID; 417355; -.
DR KEGG; gga:417355; -.
DR CTD; 23210; -.
DR VEuPathDB; HostDB:geneid_417355; -.
DR eggNOG; KOG2130; Eukaryota.
DR InParanoid; Q5ZMK5; -.
DR OrthoDB; 609279at2759; -.
DR PhylomeDB; Q5ZMK5; -.
DR PRO; PR:Q5ZMK5; -.
DR Proteomes; UP000000539; Unplaced.
DR GO; GO:0005737; C:cytoplasm; ISS:UniProtKB.
DR GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
DR GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
DR GO; GO:0005634; C:nucleus; ISS:UniProtKB.
DR GO; GO:0032451; F:demethylase activity; ISS:UniProtKB.
DR GO; GO:0032452; F:histone demethylase activity; ISS:UniProtKB.
DR GO; GO:0033746; F:histone H3-methyl-arginine-2 demethylase activity; ISS:UniProtKB.
DR GO; GO:0033749; F:histone H3-methyl-arginine-3 demethylase activity; ISS:UniProtKB.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0106140; F:P-TEFb complex binding; IBA:GO_Central.
DR GO; GO:0070815; F:peptidyl-lysine 5-dioxygenase activity; ISS:UniProtKB.
DR GO; GO:0003727; F:single-stranded RNA binding; ISS:UniProtKB.
DR GO; GO:0140537; F:transcription regulator activator activity; ISS:UniProtKB.
DR GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
DR GO; GO:0006325; P:chromatin organization; IEA:UniProtKB-KW.
DR GO; GO:0070079; P:histone H4-R3 demethylation; ISS:UniProtKB.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0018395; P:peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; ISS:UniProtKB.
DR GO; GO:0006909; P:phagocytosis; IBA:GO_Central.
DR GO; GO:0045893; P:positive regulation of transcription, DNA-templated; ISS:UniProtKB.
DR GO; GO:0006482; P:protein demethylation; ISS:UniProtKB.
DR GO; GO:0051260; P:protein homooligomerization; ISS:UniProtKB.
DR GO; GO:0048024; P:regulation of mRNA splicing, via spliceosome; ISS:UniProtKB.
DR GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
DR GO; GO:0002040; P:sprouting angiogenesis; ISS:UniProtKB.
DR InterPro; IPR003347; JmjC_dom.
DR Pfam; PF02373; JmjC; 1.
DR SMART; SM00558; JmjC; 1.
DR PROSITE; PS51184; JMJC; 1.
PE 2: Evidence at transcript level;
KW Chromatin regulator; Cytoplasm; Developmental protein; Differentiation;
KW Dioxygenase; Iron; Metal-binding; mRNA processing; mRNA splicing; Nucleus;
KW Oxidoreductase; Reference proteome; RNA-binding; Transcription;
KW Transcription regulation.
FT CHAIN 1..414
FT /note="Bifunctional arginine demethylase and lysyl-
FT hydroxylase JMJD6"
FT /id="PRO_0000129373"
FT DOMAIN 141..305
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT REGION 336..414
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 6..10
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT MOTIF 91..95
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT MOTIF 141..145
FT /note="Nuclear localization signal 3"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT MOTIF 167..170
FT /note="Nuclear localization signal 4"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT MOTIF 373..378
FT /note="Nuclear localization signal 5"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT COMPBIAS 336..360
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 184
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 187
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
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:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 197
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
FT BINDING 204
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 273
FT /ligand="Fe cation"
FT /ligand_id="ChEBI:CHEBI:24875"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT BINDING 285
FT /ligand="2-oxoglutarate"
FT /ligand_id="ChEBI:CHEBI:16810"
FT /evidence="ECO:0000250|UniProtKB:Q6NYC1"
SQ SEQUENCE 414 AA; 47760 MW; FB7EFCCF5701592D CRC64;
MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YCETFPLSPA ACKDNVERAD ALQLTVEEFV
ERYEKPYKPV VLLNAQVGWS AQEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIEY
METTRDDSPL YIFDSSYGEH PKRRKLLEDY KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP
RSGTGIHIDP LGTSAWNALV QGHKRWCLFP TSTPRELIKV AREEGGNQQD EAITWFNVIY
PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS CTNFPVVWHK
TVRGRPKLSR KWYRILKQEH PDLAALADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE
CDSGSETEGM MHRRKKRRTC SMMGNGDTTS QDDCVSKERS SSRIRESCGG RSYP
