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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)

 JMJD6_MOUSE             Reviewed;         403 AA.
Q9ERI5; A2AA26; A8Y5I2; Q80TX1;
07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
04-DEC-2007, sequence version 2.
10-MAY-2017, entry version 124.
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;
Name=Jmjd6; Synonyms=Kiaa0585, Ptdsr;
Mus musculus (Mouse).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
NCBI_TaxID=10090;
[1]
NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
STRAIN=Swiss Webster; TISSUE=Brain;
PubMed=10811223; DOI=10.1038/35011084;
Fadok V.A., Bratton D.L., Rose D.M., Pearson A., Ezekewitz R.A.,
Henson P.M.;
"A receptor for phosphatidylserine-specific clearance of apoptotic
cells.";
Nature 405:85-90(2000).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
TISSUE=Brain;
PubMed=12693553; DOI=10.1093/dnares/10.1.35;
Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S.,
Nakajima D., Nagase T., Ohara O., Koga H.;
"Prediction of the coding sequences of mouse homologues of KIAA gene:
II. The complete nucleotide sequences of 400 mouse KIAA-homologous
cDNAs identified by screening of terminal sequences of cDNA clones
randomly sampled from size-fractionated libraries.";
DNA Res. 10:35-48(2003).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=C57BL/6J;
PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S.,
She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W.,
Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T.,
Zhou S., Teague B., Potamousis K., Churas C., Place M., Herschleb J.,
Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z.,
Lindblad-Toh K., Eichler E.E., Ponting C.P.;
"Lineage-specific biology revealed by a finished genome assembly of
the mouse.";
PLoS Biol. 7:E1000112-E1000112(2009).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
STRAIN=129; TISSUE=Mammary tumor;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[5]
DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
PubMed=14645847; DOI=10.1126/science.1087621;
Li M.O., Sarkisian M.R., Mehal W.Z., Rakic P., Flavell R.A.;
"Phosphatidylserine receptor is required for clearance of apoptotic
cells.";
Science 302:1560-1563(2003).
[6]
DISRUPTION PHENOTYPE.
PubMed=14715629; DOI=10.1182/blood-2003-09-3245;
Kunisaki Y., Masuko S., Noda M., Inayoshi A., Sanui T., Harada M.,
Sasazuki T., Fukui Y.;
"Defective fetal liver erythropoiesis and T lymphopoiesis in mice
lacking the phosphatidylserine receptor.";
Blood 103:3362-3364(2004).
[7]
SUBCELLULAR LOCATION.
PubMed=14729065; DOI=10.1016/j.yexcr.2003.09.023;
Cui P., Qin B., Liu N., Pan G., Pei D.;
"Nuclear localization of the phosphatidylserine receptor protein via
multiple nuclear localization signals.";
Exp. Cell Res. 293:154-163(2004).
[8]
DISRUPTION PHENOTYPE, FUNCTION, TISSUE SPECIFICITY, AND DEVELOPMENTAL
STAGE.
PubMed=15345036; DOI=10.1186/jbiol10;
Boese J., Gruber A.D., Helming L., Schiebe S., Wegener I., Hafner M.,
Beales M., Koentgen F., Lengeling A.;
"The phosphatidylserine receptor has essential functions during
embryogenesis but not in apoptotic cell removal.";
J. Biol. 3:15.1-15.18(2004).
[9]
REVIEW ON FUNCTION.
PubMed=15453906; DOI=10.1186/jbiol14;
Williamson P., Schlegel R.A.;
"Hide and seek: the secret identity of the phosphatidylserine
receptor.";
J. Biol. 3:14.1-14.4(2004).
[10]
FUNCTION, AND INTERACTION WITH U2AF2.
PubMed=21300889; DOI=10.1073/pnas.1008098108;
Boeckel J.N., Guarani V., Koyanagi M., Roexe T., Lengeling A.,
Schermuly R.T., Gellert P., Braun T., Zeiher A., Dimmeler S.;
"Jumonji domain-containing protein 6 (Jmjd6) is required for
angiogenic sprouting and regulates splicing of VEGF-receptor 1.";
Proc. Natl. Acad. Sci. U.S.A. 108:3276-3281(2011).
[11]
INTERACTION WITH LIAT1.
PubMed=25369936; DOI=10.1073/pnas.1419587111;
Brower C.S., Rosen C.E., Jones R.H., Wadas B.C., Piatkov K.I.,
Varshavsky A.;
"Liat1, an arginyltransferase-binding protein whose evolution among
primates involved changes in the numbers of its 10-residue repeats.";
Proc. Natl. Acad. Sci. U.S.A. 111:E4936-E4945(2014).
-!- 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 and LUC7L2. 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: required for angiogenic sprouting by regulating
the pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be
necessary for the regulation of macrophage cytokine responses (By
similarity). {ECO:0000250, ECO:0000269|PubMed:15345036,
ECO:0000269|PubMed:21300889}.
-!- COFACTOR:
Name=Fe(2+); Xref=ChEBI:CHEBI:29033; Evidence={ECO:0000250};
Note=Binds 1 Fe(2+) ion per subunit. {ECO:0000250};
-!- SUBUNIT: Interacts with LUC7L2 and LUC7L3. Interacts with BRD4 (By
similarity). Interacts with U2AF2/U2AF65. Interacts with LIAT1.
{ECO:0000250, ECO:0000269|PubMed:21300889,
ECO:0000269|PubMed:25369936}.
-!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
{ECO:0000269|PubMed:14729065}. Nucleus, nucleolus {ECO:0000250}.
Note=Mainly found throughout the nucleoplasm outside of regions
containing heterochromatic DNA, with some localization in
nucleolus. During mitosis, excluded from the nucleus and reappears
in the telophase of the cell cycle (By similarity). {ECO:0000250}.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=Q9ERI5-1; Sequence=Displayed;
Name=2;
IsoId=Q9ERI5-2; Sequence=VSP_014024, VSP_014025;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: Widely expressed. Expressed in brain, eye,
spinal chord, thymus, lung, liver, kidney and intestine.
{ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:15345036}.
-!- DEVELOPMENTAL STAGE: Expressed early in development. Expressed
from embryonic stem cells and throughout embryogenesis.
{ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:15345036}.
-!- DOMAIN: The nuclear localization signal motifs are necessary and
sufficient to target it into the nucleus. {ECO:0000250}.
-!- DISRUPTION PHENOTYPE: Mice display perinatal lethality, growth
retardation, severe anemia and a delay in terminal differentiation
of the kidney, intestine, liver and lungs during embryogenesis.
Moreover, eye development can be severely disturbed, ranging from
defects in retinal differentiation to complete unilateral or
bilateral absence of eyes. According to PubMed:14645847, mice are
defective in removing apoptotic cells, especially in the lung and
brain, in which dead cells accumulate, causing abnormal
development and leading to neonatal lethality. According to
PubMed:14715629, mice lacking Jmjd6 display a reduced number of
macrophages and apoptotic cells in fetal liver. In contrast,
according to PubMed:15345036, mice show a normal engulfment of
apoptotic cells. The contradictory results concerning apoptosis
and macrophage function may be explained by the fact that the
protein plays a key role in hematopoietic differentiation.
{ECO:0000269|PubMed:14645847, ECO:0000269|PubMed:14715629,
ECO:0000269|PubMed:15345036}.
-!- 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. Phosphatidylserine receptor probably
participates in apoptotic cell phagocytosis. This protein was
identified using phage display expressing mAb 217, an antibody
that specifically recognizes phosphatidylserine receptor. However,
its nuclear localization and the fact that mAb 217 antibody still
recognizes the phosphatidylserine receptor in mice lacking Jmjd6,
strongly suggest that it does not constitute the receptor for
phosphatidylserine and is not involved in apoptotic cell removal.
{ECO:0000305}.
-!- SEQUENCE CAUTION:
Sequence=BAC65599.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms
Distributed under the Creative Commons Attribution-NoDerivs License
-----------------------------------------------------------------------
EMBL; AF304118; AAG27719.1; -; mRNA.
EMBL; AK122317; BAC65599.1; ALT_INIT; mRNA.
EMBL; AL645542; CAP19369.1; -; Genomic_DNA.
EMBL; BC056629; AAH56629.1; -; mRNA.
CCDS; CCDS25678.1; -. [Q9ERI5-1]
RefSeq; NP_203971.2; NM_033398.2. [Q9ERI5-1]
UniGene; Mm.481684; -.
ProteinModelPortal; Q9ERI5; -.
SMR; Q9ERI5; -.
STRING; 10090.ENSMUSP00000047570; -.
iPTMnet; Q9ERI5; -.
PhosphoSitePlus; Q9ERI5; -.
PaxDb; Q9ERI5; -.
PRIDE; Q9ERI5; -.
Ensembl; ENSMUST00000047616; ENSMUSP00000047570; ENSMUSG00000056962. [Q9ERI5-1]
GeneID; 107817; -.
KEGG; mmu:107817; -.
UCSC; uc007mmi.1; mouse. [Q9ERI5-1]
UCSC; uc007mmj.1; mouse. [Q9ERI5-2]
CTD; 23210; -.
MGI; MGI:1858910; Jmjd6.
eggNOG; KOG2130; Eukaryota.
eggNOG; ENOG410XQCR; LUCA.
GeneTree; ENSGT00530000063579; -.
HOGENOM; HOG000265824; -.
HOVERGEN; HBG054774; -.
InParanoid; Q9ERI5; -.
KO; K11323; -.
OrthoDB; EOG091G0AJ6; -.
PhylomeDB; Q9ERI5; -.
TreeFam; TF314988; -.
Reactome; R-MMU-3214842; HDMs demethylate histones.
ChiTaRS; Jmjd6; mouse.
PRO; PR:Q9ERI5; -.
Proteomes; UP000000589; Chromosome 11.
Bgee; ENSMUSG00000056962; -.
CleanEx; MM_JMJD6; -.
ExpressionAtlas; Q9ERI5; baseline and differential.
Genevisible; Q9ERI5; MM.
GO; GO:0005829; C:cytosol; IDA:MGI.
GO; GO:0030529; C:intracellular ribonucleoprotein complex; IDA:MGI.
GO; GO:0005730; C:nucleolus; ISS:UniProtKB.
GO; GO:0005654; C:nucleoplasm; IDA:MGI.
GO; GO:0005634; C:nucleus; IDA:UniProtKB.
GO; GO:0005886; C:plasma membrane; IDA:MGI.
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:0042802; F:identical protein binding; IDA:MGI.
GO; GO:0005506; F:iron ion binding; ISO:MGI.
GO; GO:0070815; F:peptidyl-lysine 5-dioxygenase activity; ISS:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IDA:MGI.
GO; GO:0004872; F:receptor activity; IDA:MGI.
GO; GO:0003723; F:RNA binding; IDA:MGI.
GO; GO:0003727; F:single-stranded RNA binding; ISS:UniProtKB.
GO; GO:0043277; P:apoptotic cell clearance; IMP:MGI.
GO; GO:0001568; P:blood vessel development; IMP:MGI.
GO; GO:0007166; P:cell surface receptor signaling pathway; IDA:MGI.
GO; GO:0048821; P:erythrocyte development; IMP:MGI.
GO; GO:0007507; P:heart development; IMP:MGI.
GO; GO:0070078; P:histone H3-R2 demethylation; ISO:MGI.
GO; GO:0070079; P:histone H4-R3 demethylation; ISO:MGI.
GO; GO:0001822; P:kidney development; IMP:MGI.
GO; GO:0030324; P:lung development; IMP:MGI.
GO; GO:0042116; P:macrophage activation; IMP:MGI.
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:0043654; P:recognition of apoptotic cell; IDA:MGI.
GO; GO:0048024; P:regulation of mRNA splicing, via spliceosome; IMP:UniProtKB.
GO; GO:0006355; P:regulation of transcription, DNA-templated; IEA:UniProtKB-KW.
GO; GO:0060041; P:retina development in camera-type eye; IMP:MGI.
GO; GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
GO; GO:0002040; P:sprouting angiogenesis; IMP:UniProtKB.
GO; GO:0033077; P:T cell differentiation in thymus; IMP:MGI.
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.
1: Evidence at protein 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_0000129370.
DOMAIN 141 305 JmjC. {ECO:0000255|PROSITE-
ProRule:PRU00538}.
MOTIF 6 10 Nuclear localization signal 1.
{ECO:0000250}.
MOTIF 91 95 Nuclear localization signal 2.
{ECO:0000250}.
MOTIF 141 145 Nuclear localization signal 3.
{ECO:0000250}.
MOTIF 167 170 Nuclear localization signal 4.
{ECO:0000250}.
MOTIF 373 378 Nuclear localization signal 5.
{ECO:0000250}.
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 270 298 GWWHVVLNLDTTIAITQNFASSTNFPVVW -> IDELEETI
PVRPSSDWSGLVLYCHFGVES (in isoform 2).
{ECO:0000303|PubMed:12693553}.
/FTId=VSP_014024.
VAR_SEQ 299 403 Missing (in isoform 2).
{ECO:0000303|PubMed:12693553}.
/FTId=VSP_014025.
CONFLICT 43 43 P -> S (in Ref. 1; AAG27719 and 4;
AAH56629). {ECO:0000305}.
SEQUENCE 403 AA; 46567 MW; D440E880B2F1BB37 CRC64;
MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESYPLNPA AVPDNVERAD ALQLSVKEFV
ERYERPYKPV VLLNAQEGWS AQEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIEY
MESTRDDSPL YIFDSSYGEH PKRRKLLEDY KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP
RSGTGIHIDP LGTSAWNALV QGHKRWCLFP TNTPRELIKV TREEGGNQQD EAITWFNVIY
PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK
TVRGRPKLSR KWYRILKQEH PELAVLADAV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE
CESGSEGDGT THRRKKRRTC SMVGNGDTTS QDDCVSKERS SSR


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