JMD6B_XENLA
ID JMD6B_XENLA Reviewed; 403 AA.
AC Q7ZX37;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 79.
DE RecName: Full=Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6-B;
DE EC=1.14.11.-;
DE AltName: Full=Histone arginine demethylase JMJD6-B;
DE AltName: Full=JmjC domain-containing protein 6-B;
DE AltName: Full=Jumonji domain-containing protein 6-B;
DE AltName: Full=Lysyl-hydroxylase JMJD6-B;
DE AltName: Full=Peptide-lysine 5-dioxygenase JMJD6-B;
DE AltName: Full=Phosphatidylserine receptor-B;
DE Short=Protein PTDSR-B;
GN Name=jmjd6-b; Synonyms=ptdsr-b;
OS Xenopus laevis (African clawed frog).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Amphibia;
OC Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae; Xenopus; Xenopus.
OX NCBI_TaxID=8355;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Xenopus Gene Collection (XGC) project;
RL Submitted (JAN-2003) to the EMBL/GenBank/DDBJ databases.
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}.
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; BC045252; AAH45252.1; -; mRNA.
DR RefSeq; NP_001080514.1; NM_001087045.1.
DR AlphaFoldDB; Q7ZX37; -.
DR SMR; Q7ZX37; -.
DR DNASU; 380206; -.
DR GeneID; 380206; -.
DR KEGG; xla:380206; -.
DR CTD; 380206; -.
DR Xenbase; XB-GENE-6078236; jmjd6.S.
DR OMA; AVSENFW; -.
DR OrthoDB; 609279at2759; -.
DR Proteomes; UP000186698; Chromosome 9_10S.
DR Bgee; 380206; Expressed in egg cell and 19 other tissues.
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:0070815; F:peptidyl-lysine 5-dioxygenase activity; ISS:UniProtKB.
DR GO; GO:0003727; F:single-stranded RNA binding; 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: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..403
FT /note="Bifunctional arginine demethylase and lysyl-
FT hydroxylase JMJD6-B"
FT /id="PRO_0000129376"
FT DOMAIN 141..305
FT /note="JmjC"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00538"
FT REGION 336..403
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..365
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 403 AA; 46516 MW; 5759CD6530E00F1B CRC64;
MNHKSKKRIK EAKRSARPEL KDSQDWCRHN YCEVFSLNPS TVLDNVERVD AAQLTTEEFI
ERYEKPYKPV VIINATAGWP ANEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIDY
MEGTRDDSPL YIFDSSYGEH PKRKKILEDY EVPKYFRDDL FQFTGEKRRP PYRWFVMGPP
RSGTGIHIDP LGTSAWNSLV HGHKRWCLFP TNTPRELIKV TRDEGGNQQD EAITWFNVVY
PRTQLPSWPP EFKPLEILQK PGETVFVPGG WWHVVLNFDT AIAVTQNFAS CSNFPVVWHK
TVRGRPKLSR KWYRILKQER PELAALADTV DLQESTGIAS DSSSDSSSSS SSSSSESCSE
DDSSSGAEMM SRRKKKRRLC NGMGNGDITT QDDCASKERS SSR
