Q6AYK2 (JMJD6_RAT) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
EC=1.14.11.-

Alternative name(s):
Histone arginine demethylase JMJD6
JmjC domain-containing protein 6
Jumonji domain-containing protein 6
Lysyl-hydroxylase JMJD6
Peptide-lysine 5-dioxygenase JMJD6
Phosphatidylserine receptor
Short name=Protein PTDSR

Gene names

Name:	Jmjd6
Synonyms:	Ptdsr

Organism

Rattus norvegicus (Rat)

Taxonomic identifier

10116 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length	403 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

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 a 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.
Cofactor	Binds 1 Fe2+ ion per subunit By similarity.
Subunit structure	Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65 By similarity.
Subcellular location	Nucleus › nucleoplasm By similarity. Nucleus › nucleolus By similarity. 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.
Domain	The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus By similarity.
Sequence similarities	Belongs to the JMJD6 family. Contains 1 JmjC domain.

Ontologies

Keywords
Biological process	Differentiation Transcription Transcription regulation mRNA processing mRNA splicing
Cellular component	Nucleus
Ligand	Iron Metal-binding RNA-binding
Molecular function	Chromatin regulator Developmental protein Dioxygenase Oxidoreductase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW cell differentiation Inferred from electronic annotation. Source: UniProtKB-KW mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine Inferred from sequence or structural similarity. Source: UniProtKB regulation of nuclear mRNA splicing, via spliceosome Inferred from sequence or structural similarity. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW sprouting angiogenesis Inferred from sequence or structural similarity. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	nucleolus Inferred from sequence or structural similarity. Source: UniProtKB nucleoplasm Inferred from sequence or structural similarity. Source: UniProtKB
Molecular function	histone demethylase activity (H3-R2 specific) Inferred from sequence or structural similarity. Source: UniProtKB histone demethylase activity (H4-R3 specific) Inferred from sequence or structural similarity. Source: UniProtKB metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen Inferred from electronic annotation. Source: UniProtKB-KW peptidyl-lysine 5-dioxygenase activity Inferred from sequence or structural similarity. Source: UniProtKB single-stranded RNA binding Inferred from sequence or structural similarity. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 403	403	Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6		PRO_0000129372
Regions
	Domain	141 – 305	165	JmjC
	Motif	6 – 10	5	Nuclear localization signal 1 By similarity
	Motif	91 – 95	5	Nuclear localization signal 2 By similarity
	Motif	141 – 145	5	Nuclear localization signal 3 By similarity
	Motif	167 – 170	4	Nuclear localization signal 4 By similarity
	Motif	373 – 378	6	Nuclear localization signal 5 By similarity
	Compositional bias	340 – 365	26	Ser-rich
Sites
	Metal binding	187	1	Iron; catalytic By similarity
	Metal binding	189	1	Iron; catalytic By similarity
	Metal binding	273	1	Iron; catalytic By similarity
	Binding site	184	1	Substrate By similarity
	Binding site	197	1	2-oxoglutarate By similarity
	Binding site	204	1	Substrate By similarity
	Binding site	285	1	2-oxoglutarate By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q6AYK2 [UniParc]. Last modified June 7, 2005. Version 2. Checksum: 629EE773BD0DB737	FASTA	403	46,540
	10 20 30 40 50 60 MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESYPLSPA AVPDNVERAD ALQLSVKEFV 70 80 90 100 110 120 ERYERPYKPV VLLNAQEGWS AQEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIEY 130 140 150 160 170 180 MESTRDDSPL YIFDSSYGEH PKRRKLLEDY KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP 190 200 210 220 230 240 RSGTGIHIDP LGTSAWNALV QGHKRWCLFP TNTPRELIKV TREEGGNQQD EAITWFNVIY 250 260 270 280 290 300 PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK 310 320 330 340 350 360 TVRGRPKLSR KWYRILKQEH PELAVLADAV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE 370 380 390 400 CESGSEGDGT THRRKKRRTC SMVGNGDTTS QDDCVSKERS SSR

References

[1]

"Genome sequence of the Brown Norway rat yields insights into mammalian evolution." Gibbs R.A., Weinstock G.M., Metzker M.L., Muzny D.M., Sodergren E.J., Scherer S., Scott G., Steffen D., Worley K.C., Burch P.E., Okwuonu G., Hines S., Lewis L., Deramo C., Delgado O., Dugan-Rocha S., Miner G., Morgan M. , Hawes A., Gill R., Holt R.A., Adams M.D., Amanatides P.G., Baden-Tillson H., Barnstead M., Chin S., Evans C.A., Ferriera S., Fosler C., Glodek A., Gu Z., Jennings D., Kraft C.L., Nguyen T., Pfannkoch C.M., Sitter C., Sutton G.G., Venter J.C., Woodage T., Smith D., Lee H.-M., Gustafson E., Cahill P., Kana A., Doucette-Stamm L., Weinstock K., Fechtel K., Weiss R.B., Dunn D.M., Green E.D., Blakesley R.W., Bouffard G.G., De Jong P.J., Osoegawa K., Zhu B., Marra M., Schein J., Bosdet I., Fjell C., Jones S., Krzywinski M., Mathewson C., Siddiqui A., Wye N., McPherson J., Zhao S., Fraser C.M., Shetty J., Shatsman S., Geer K., Chen Y., Abramzon S., Nierman W.C., Havlak P.H., Chen R., Durbin K.J., Egan A., Ren Y., Song X.-Z., Li B., Liu Y., Qin X., Cawley S., Cooney A.J., D'Souza L.M., Martin K., Wu J.Q., Gonzalez-Garay M.L., Jackson A.R., Kalafus K.J., McLeod M.P., Milosavljevic A., Virk D., Volkov A., Wheeler D.A., Zhang Z., Bailey J.A., Eichler E.E., Tuzun E., Birney E., Mongin E., Ureta-Vidal A., Woodwark C., Zdobnov E., Bork P., Suyama M., Torrents D., Alexandersson M., Trask B.J., Young J.M., Huang H., Wang H., Xing H., Daniels S., Gietzen D., Schmidt J., Stevens K., Vitt U., Wingrove J., Camara F., Mar Alba M., Abril J.F., Guigo R., Smit A., Dubchak I., Rubin E.M., Couronne O., Poliakov A., Huebner N., Ganten D., Goesele C., Hummel O., Kreitler T., Lee Y.-A., Monti J., Schulz H., Zimdahl H., Himmelbauer H., Lehrach H., Jacob H.J., Bromberg S., Gullings-Handley J., Jensen-Seaman M.I., Kwitek A.E., Lazar J., Pasko D., Tonellato P.J., Twigger S., Ponting C.P., Duarte J.M., Rice S., Goodstadt L., Beatson S.A., Emes R.D., Winter E.E., Webber C., Brandt P., Nyakatura G., Adetobi M., Chiaromonte F., Elnitski L., Eswara P., Hardison R.C., Hou M., Kolbe D., Makova K., Miller W., Nekrutenko A., Riemer C., Schwartz S., Taylor J., Yang S., Zhang Y., Lindpaintner K., Andrews T.D., Caccamo M., Clamp M., Clarke L., Curwen V., Durbin R.M., Eyras E., Searle S.M., Cooper G.M., Batzoglou S., Brudno M., Sidow A., Stone E.A., Payseur B.A., Bourque G., Lopez-Otin C., Puente X.S., Chakrabarti K., Chatterji S., Dewey C., Pachter L., Bray N., Yap V.B., Caspi A., Tesler G., Pevzner P.A., Haussler D., Roskin K.M., Baertsch R., Clawson H., Furey T.S., Hinrichs A.S., Karolchik D., Kent W.J., Rosenbloom K.R., Trumbower H., Weirauch M., Cooper D.N., Stenson P.D., Ma B., Brent M., Arumugam M., Shteynberg D., Copley R.R., Taylor M.S., Riethman H., Mudunuri U., Peterson J., Guyer M., Felsenfeld A., Old S., Mockrin S., Collins F.S. Nature 428:493-521(2004) [PubMed: 15057822] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: Brown Norway.

[2]

"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Testis.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AABR03075342 Genomic DNA. No translation available. AABR03077255 Genomic DNA. No translation available. BC079012 mRNA. Translation: AAH79012.1.
IPI	IPI00464733.
RefSeq	NP_001012143.2. NM_001012143.2.
UniGene	Rn.19923.
3D structure databases
ProteinModelPortal	Q6AYK2.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	360665.
KEGG	rno:360665.
UCSC	BC079012. rat.
Organism-specific databases
CTD	23210.
RGD	1305395. Jmjd6.
Phylogenomic databases
eggNOG	roNOG07926.
HOVERGEN	HBG054774.
Gene expression databases
Genevestigator	Q6AYK2.
Family and domain databases
InterPro	IPR013129. TF_JmjC. IPR003347. TF_JmjC_AAH. [Graphical view]
KO	K11323.
Pfam	PF02373. JmjC. 1 hit. [Graphical view]
SMART	SM00558. JmjC. 1 hit. [Graphical view]
PROSITE	PS51184. JMJC. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	673684.

Entry information

Entry name

JMJD6_RAT

Accession

Primary (citable) accession number: Q6AYK2

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	June 7, 2005
Last modified:	December 14, 2011
This is version 56 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program