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Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 (EC 1.14.11.-) (Histone arginine demethylase JMJD6) (JmjC domain-containing protein 6) (Jumonji domain-containing protein 6) (Lysyl-hydroxylase JMJD6) (Peptide-lysine 5-dioxygenase JMJD6) (Phosphatidylserine receptor) (Protein PTDSR) (zfpsr)

 JMJD6_DANRE             Reviewed;         403 AA.
Q6PFM0; Q8JI07; Q8JI08;
07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
17-APR-2007, sequence version 2.
30-AUG-2017, entry version 85.
RecName: Full=Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6;
EC=1.14.11.-;
AltName: Full=Histone arginine demethylase JMJD6;
AltName: Full=JmjC domain-containing protein 6;
AltName: Full=Jumonji domain-containing protein 6;
AltName: Full=Lysyl-hydroxylase JMJD6;
AltName: Full=Peptide-lysine 5-dioxygenase JMJD6;
AltName: Full=Phosphatidylserine receptor;
Short=Protein PTDSR;
Short=zfpsr;
Name=jmjd6; Synonyms=psr, ptdsr; ORFNames=zgc:66264;
Danio rerio (Zebrafish) (Brachydanio rerio).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
Cyprinidae; Danio.
NCBI_TaxID=7955;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY,
DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
TISSUE=Embryo;
PubMed=15469976; DOI=10.1242/dev.01409;
Hong J.-R., Lin G.-H., Lin C.J.-F., Wang W.-P., Lee C.-C., Lin T.-L.,
Wu J.-L.;
"Phosphatidylserine receptor is required for the engulfment of dead
apoptotic cells and for normal embryonic development in zebrafish.";
Development 131:5417-5427(2004).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=SJD;
NIH - Zebrafish Gene Collection (ZGC) project;
Submitted (SEP-2003) to the EMBL/GenBank/DDBJ databases.
-!- FUNCTION: Dioxygenase that can both act as a histone arginine
demethylase and a lysyl-hydroxylase. Acts as a lysyl-hydroxylase
that catalyzes 5-hydroxylation on specific lysine residues of
target proteins such as u2af2/u2af65. Acts as a regulator of RNA
splicing by mediating 5-hydroxylation of u2af2/u2af65, affecting
the pre-mRNA splicing activity of u2af2/u2af65. In addition to
peptidyl-lysine 5-dioxygenase activity, may act as an RNA
hydroxylase, as suggested by its ability to bind single strand
RNA. Also acts as an arginine demethylase which demethylates
histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me),
thereby playing a role in histone code. However, histone arginine
demethylation may not constitute the primary activity in vivo. Has
no histone lysine demethylase activity. Required for
differentiation of multiple organs during embryogenesis. Acts as a
key regulator of hematopoietic differentiation (By similarity).
{ECO:0000250}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm {ECO:0000250}. Nucleus,
nucleolus {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Comment=Long.;
Name=1;
IsoId=Q6PFM0-1; Sequence=Displayed;
Name=2; Synonyms=Short;
IsoId=Q6PFM0-2; Sequence=VSP_014026, VSP_014027;
-!- TISSUE SPECIFICITY: After the somite segmentation period, it is
apparent throughout the embryo and the hatching gland. At the
larval (3 dpf) stage, it is detected in the heart and kidney.
{ECO:0000269|PubMed:15469976}.
-!- DEVELOPMENTAL STAGE: Expressed in embryos from the one-cell
developmental stage to the 3 days post-fertilization (dpf) larval
stage. {ECO:0000269|PubMed:15469976}.
-!- DISRUPTION PHENOTYPE: Fishes display an accumulation of a large
number of dead apoptotic cells in whole early embryo. These cells
interfere with embryonic cell migration. In addition, normal
development of the somite, brain, heart and notochord are
sequentially disrupted up to 24 hours post-fertilization.
{ECO:0000269|PubMed:15469976}.
-!- SIMILARITY: Belongs to the JMJD6 family. {ECO:0000305}.
-!- CAUTION: Was initially thought to constitute the
phosphatidylserine receptor, a receptor that mediates recognition
of phosphatidylserine, a specific marker only present at the
surface of apoptotic cells, and participates in apoptotic cell
phagocytosis. However, some results strongly suggest that it does
not constitute the receptor for phosphatidylserine and is not
involved in apoptotic cell removal. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; AF401484; AAM90671.1; -; mRNA.
EMBL; AF401485; AAM90672.1; -; mRNA.
EMBL; BC057498; AAH57498.1; -; mRNA.
RefSeq; NP_739567.3; NM_170761.3. [Q6PFM0-1]
UniGene; Dr.86243; -.
ProteinModelPortal; Q6PFM0; -.
SMR; Q6PFM0; -.
STRING; 7955.ENSDARP00000107901; -.
PaxDb; Q6PFM0; -.
PRIDE; Q6PFM0; -.
Ensembl; ENSDART00000157822; ENSDARP00000139813; ENSDARG00000102896. [Q6PFM0-1]
Ensembl; ENSDART00000171922; ENSDARP00000141713; ENSDARG00000102896. [Q6PFM0-1]
GeneID; 266962; -.
KEGG; dre:266962; -.
CTD; 23210; -.
ZFIN; ZDB-GENE-040426-17; jmjd6.
eggNOG; KOG2130; Eukaryota.
eggNOG; ENOG410XQCR; LUCA.
GeneTree; ENSGT00530000063579; -.
HOGENOM; HOG000265824; -.
HOVERGEN; HBG054774; -.
InParanoid; Q6PFM0; -.
KO; K11323; -.
OMA; PTHTPRE; -.
OrthoDB; EOG091G0AJ6; -.
PhylomeDB; Q6PFM0; -.
TreeFam; TF314988; -.
Reactome; R-DRE-3214842; HDMs demethylate histones.
PRO; PR:Q6PFM0; -.
Proteomes; UP000000437; Chromosome 3.
Bgee; ENSDARG00000102896; -.
GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
GO; GO:0005654; C:nucleoplasm; ISS:UniProtKB.
GO; GO:0005634; C:nucleus; ISS:UniProtKB.
GO; GO:0033746; F:histone demethylase activity (H3-R2 specific); ISS:UniProtKB.
GO; GO:0033749; F:histone demethylase activity (H4-R3 specific); ISS:UniProtKB.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0070815; F:peptidyl-lysine 5-dioxygenase activity; ISS:UniProtKB.
GO; GO:0003727; F:single-stranded RNA binding; ISS:UniProtKB.
GO; GO:0030154; P:cell differentiation; IEA:UniProtKB-KW.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0018395; P:peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; ISS:UniProtKB.
GO; GO:0006909; P:phagocytosis; IMP:ZFIN.
GO; GO:0048024; P:regulation of mRNA splicing, via spliceosome; ISS:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
GO; GO:0002040; P:sprouting angiogenesis; ISS:UniProtKB.
GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-KW.
InterPro; IPR003347; JmjC_dom.
Pfam; PF02373; JmjC; 1.
SMART; SM00558; JmjC; 1.
PROSITE; PS51184; JMJC; 1.
2: Evidence at transcript level;
Alternative splicing; Chromatin regulator; Complete proteome;
Developmental protein; Differentiation; Dioxygenase; Iron;
Metal-binding; mRNA processing; mRNA splicing; Nucleus;
Oxidoreductase; Reference proteome; RNA-binding; Transcription;
Transcription regulation.
CHAIN 1 403 Bifunctional arginine demethylase and
lysyl-hydroxylase JMJD6.
/FTId=PRO_0000129374.
DOMAIN 141 305 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
COMPBIAS 340 365 Ser-rich.
METAL 187 187 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 189 189 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
METAL 273 273 Iron; catalytic. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
BINDING 184 184 Substrate. {ECO:0000250}.
BINDING 197 197 2-oxoglutarate. {ECO:0000250}.
BINDING 204 204 Substrate. {ECO:0000250}.
BINDING 285 285 2-oxoglutarate. {ECO:0000250}.
VAR_SEQ 214 226 PRELIKVTRDEGG -> HTRFIIFNKLVCE (in
isoform 2).
{ECO:0000303|PubMed:15469976}.
/FTId=VSP_014026.
VAR_SEQ 227 403 Missing (in isoform 2).
{ECO:0000303|PubMed:15469976}.
/FTId=VSP_014027.
CONFLICT 385 385 N -> S (in Ref. 2; AAH57498).
{ECO:0000305}.
SEQUENCE 403 AA; 46687 MW; 9E0F7E1C8AFE0194 CRC64;
MNHKSKKRIK EAKRSARPEL KDSSDWTKHE YCKSFDLSHR SVKDNVERAD VQRLSPEEFI
QRFEKPYKPV VLLNVEDSWP AREKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYVEY
LESTHDDSPL YIFDSSFGEH AKRRKLLEDY QVPLFFRDDL FQFAGEKRRP PYRWFVMGPA
RSGTGIHIDP LGTSAWNALV QGHKRWCLFP THTPRELIKV TRDEGGNQQD EAITWFNVIY
PRTQQSTWPD EFRPLEILQR PGETVFVPGG WWHVVLNLDT TIAVTQNFAS TTNFPIVWHK
TVRGRPKLSR KWYRILKQER PDIAAIADKV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE
ADSGSEGDAM THRRKKRRTG GMMGNGDITS QDDCASKERS SSR


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