Q6NYC1 (JMJD6_HUMAN) 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:	KIAA0585, PTDSR

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	403 AA.
Sequence status	Complete.
Protein existence	Evidence at protein 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. Ref.10 Ref.11 Ref.12 Ref.14 Ref.15
Cofactor	Binds 1 Fe2+ ion per subunit. Ref.11
Subunit structure	Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65. Ref.11
Subcellular location	Nucleus › nucleoplasm. Nucleus › nucleolus. 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. Ref.7 Ref.12
Tissue specificity	Highly expressed in the heart, skeletal muscle and kidney. Expressed at moderate or low level in brain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testis and ovary. Up-regulated in many patients with chronic pancreatitis. Expressed in nursing thymic epithelial cells. Ref.2 Ref.8 Ref.9
Induction	Up-regulated upon cytokine treatment, but not upon TNF treatment. Ref.8
Domain	The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus.
Sequence similarities	Belongs to the JMJD6 family. Contains 1 JmjC domain.
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.
Biophysicochemical properties	Kinetic parameters: KM=39 µM for 2-oxoglutarate Ref.14
Sequence caution	The sequence AAH47003.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened. The sequence BAA25511.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Biological process	Differentiation Transcription Transcription regulation mRNA processing mRNA splicing
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Ligand	Iron Metal-binding RNA-binding
Molecular function	Chromatin regulator Developmental protein Dioxygenase Oxidoreductase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	RNA splicing Inferred from electronic annotation. Source: UniProtKB-KW T cell differentiation in thymus Inferred from electronic annotation. Source: Compara apoptotic process Inferred from electronic annotation. Source: Compara cell surface receptor signaling pathway Inferred from electronic annotation. Source: Compara erythrocyte development Inferred from electronic annotation. Source: Compara heart development Inferred from electronic annotation. Source: Compara kidney development Inferred from electronic annotation. Source: Compara lung development Inferred from electronic annotation. Source: Compara mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW macrophage activation Inferred from electronic annotation. Source: Compara peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine Inferred from direct assay Ref.11. Source: UniProtKB recognition of apoptotic cell Inferred from electronic annotation. Source: Compara regulation of mRNA splicing, via spliceosome Inferred from mutant phenotype Ref.11. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW retina development in camera-type eye Inferred from electronic annotation. Source: Compara 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 direct assay Ref.12. Source: UniProtKB nucleoplasm Inferred from direct assay Ref.12. Source: UniProtKB plasma membrane Inferred from electronic annotation. Source: Compara
Molecular_function	histone demethylase activity (H3-R2 specific) Inferred from direct assay Ref.10. Source: UniProtKB histone demethylase activity (H4-R3 specific) Inferred from direct assay Ref.10. Source: UniProtKB identical protein binding Inferred from direct assay PubMed 17534701. Source: BHF-UCL iron ion binding Inferred from direct assay Ref.15. Source: UniProtKB 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 direct assay Ref.11. Source: UniProtKB receptor activity Inferred from electronic annotation. Source: Compara single-stranded RNA binding Inferred from direct assay Ref.15. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q6NYC1-1)

Also known as: Alpha;

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q6NYC1-2)

Also known as: Beta;

The sequence of this isoform differs from the canonical sequence as follows:
     361-402: Missing.
     403-403: R → RIRDTCGGRAHP

Isoform 3 (identifier: Q6NYC1-3)

The sequence of this isoform differs from the canonical sequence as follows:
     403-403: R → RIRDTCGGRAHP

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_0000129369

Regions

Domain

141 – 305

165

JmjC

Motif

6 – 10

5

Nuclear localization signal 1 Ref.7

Motif

91 – 95

5

Nuclear localization signal 2 Ref.7

Motif

141 – 145

5

Nuclear localization signal 3 Ref.7

Motif

167 – 170

4

Nuclear localization signal 4 Ref.7

Motif

373 – 378

6

Nuclear localization signal 5 Ref.7

Compositional bias

340 – 365

26

Ser-rich

Sites

Metal binding

187

1

Iron; catalytic

Metal binding

189

1

Iron; catalytic

Metal binding

273

1

Iron; catalytic

Binding site

184

1

Substrate By similarity

Binding site

197

1

2-oxoglutarate

Binding site

204

1

Substrate By similarity

Binding site

285

1

2-oxoglutarate

Natural variations

Alternative sequence

361 – 402

42

Missing in isoform 2.

VSP_014022

Alternative sequence

403

1

R → RIRDTCGGRAHP in isoform 2 and isoform 3.

VSP_014023

Experimental info

Mutagenesis

131

1

Y → F: Abolishes 2-oxoglutarate-binding and enzyme activity. Ref.14

Mutagenesis

187

1

H → A: Loss of catalytic activity; when associated with A-189 and A-273. Ref.10 Ref.11

Mutagenesis

189

1

D → A: Loss of catalytic activity; when associated with A-187 and A-273. Ref.10 Ref.11

Mutagenesis

204

1

K → A: Impairs enzyme activity without affecting 2-oxoglutarate-binding. Ref.14

Mutagenesis

231

1

E → A: Impairs both hydroxylation activity and 2-oxoglutarate turnover assays. Ref.14

Mutagenesis

273

1

H → A: Loss of catalytic activity; when associated with A-187 and A-189. Ref.10

Mutagenesis

285

1

T → A: Impairs enzyme activity and 2-oxoglutarate-binding. Ref.14

Mutagenesis

287

1

N → A: Impairs enzyme activity. Ref.14

Sequence conflict

136

1

S → G in BAG51050. Ref.3

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

403

Helix Strand Turn

Details...

Helix

3 – 16

14

Helix

23 – 27

5

Helix

31 – 34

4

Helix

39 – 41

3

Beta strand

48 – 50

3

Helix

51 – 53

3

Helix

56 – 62

7

Turn

63 – 67

5

Beta strand

70 – 74

5

Turn

75 – 78

4

Helix

81 – 84

4

Helix

87 – 93

7

Beta strand

98 – 103

6

Beta strand

109 – 113

5

Helix

114 – 123

10

Beta strand

132 – 135

4

Helix

137 – 139

3

Helix

143 – 149

7

Helix

154 – 156

3

Helix

160 – 164

5

Turn

166 – 168

3

Beta strand

173 – 178

6

Beta strand

183 – 187

5

Helix

190 – 192

3

Beta strand

194 – 202

9

Beta strand

204 – 209

6

Helix

215 – 218

4

Helix

222 – 225

4

Helix

226 – 228

3

Helix

232 – 238

7

Helix

240 – 244

5

Helix

250 – 252

3

Beta strand

255 – 259

5

Beta strand

264 – 267

4

Beta strand

272 – 279

8

Beta strand

281 – 288

8

Turn

291 – 293

3

Helix

294 – 304

11

Helix

306 – 319

14

Helix

321 – 333

13

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 (Alpha) [UniParc]. Last modified July 5, 2004. Version 1. Checksum: 9C9AADA98B24B035	FASTA	403	46,462
	10 20 30 40 50 60 MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESFSLSPA AVADNVERAD ALQLSVEEFV 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 TSTPRELIKV TRDEGGNQQD EAITWFNVIY 250 260 270 280 290 300 PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK 310 320 330 340 350 360 TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE 370 380 390 400 CESGSEGDGT VHRRKKRRTC SMVGNGDTTS QDDCVSKERS SSR
	Isoform 2 (Beta) [UniParc]. Checksum: 14154B874F1983DF	FASTA	372	43,109
	10 20 30 40 50 60 MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESFSLSPA AVADNVERAD ALQLSVEEFV 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 TSTPRELIKV TRDEGGNQQD EAITWFNVIY 250 260 270 280 290 300 PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK 310 320 330 340 350 360 TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE 370 RIRDTCGGRA HP
	Isoform 3 [UniParc]. Checksum: CD586580857C6C46	FASTA	414	47,626
	10 20 30 40 50 60 MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESFSLSPA AVADNVERAD ALQLSVEEFV 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 TSTPRELIKV TRDEGGNQQD EAITWFNVIY 250 260 270 280 290 300 PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK 310 320 330 340 350 360 TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE 370 380 390 400 410 CESGSEGDGT VHRRKKRRTC SMVGNGDTTS QDDCVSKERS SSRIRDTCGG RAHP

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Identification of an alternative form of phosphatidylserine receptor." Izawa M., Takahashi M. Submitted (OCT-2001) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2). Tissue: Stomach cancer.
[2]	"Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro." Nagase T., Ishikawa K., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O. DNA Res. 5:31-39(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 3), TISSUE SPECIFICITY. Tissue: Brain.
[3]	"Complete sequencing and characterization of 21,243 full-length human cDNAs." Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S. Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3). Tissue: Brain and Embryo.
[4]	"DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage." Zody M.C., Garber M., Adams D.J., Sharpe T., Harrow J., Lupski J.R., Nicholson C., Searle S.M., Wilming L., Young S.K., Abouelleil A., Allen N.R., Bi W., Bloom T., Borowsky M.L., Bugalter B.E., Butler J., Chang J.L. , Chen C.-K., Cook A., Corum B., Cuomo C.A., de Jong P.J., DeCaprio D., Dewar K., FitzGerald M., Gilbert J., Gibson R., Gnerre S., Goldstein S., Grafham D.V., Grocock R., Hafez N., Hagopian D.S., Hart E., Norman C.H., Humphray S., Jaffe D.B., Jones M., Kamal M., Khodiyar V.K., LaButti K., Laird G., Lehoczky J., Liu X., Lokyitsang T., Loveland J., Lui A., Macdonald P., Major J.E., Matthews L., Mauceli E., McCarroll S.A., Mihalev A.H., Mudge J., Nguyen C., Nicol R., O'Leary S.B., Osoegawa K., Schwartz D.C., Shaw-Smith C., Stankiewicz P., Steward C., Swarbreck D., Venkataraman V., Whittaker C.A., Yang X., Zimmer A.R., Bradley A., Hubbard T., Birren B.W., Rogers J., Lander E.S., Nusbaum C. Nature 440:1045-1049(2006) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]	Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C. Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]	"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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Skin and Uterus.
[7]	"Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals." Cui P., Qin B., Liu N., Pan G., Pei D. Exp. Cell Res. 293:154-163(2004) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, NUCLEAR LOCALIZATION SIGNALS.
[8]	"Phosphatidylserine receptor cooperates with high-density lipoprotein receptor in recognition of apoptotic cells by thymic nurse cells." Cao W.M., Murao K., Imachi H., Hiramine C., Abe H., Yu X., Dobashi H., Wong N.C.W., Takahara J., Ishida T. J. Mol. Endocrinol. 32:497-505(2004) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY, INDUCTION.
[9]	"Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role." Koeninger J., Balaz P., Wagner M., Shi X., Cima I., Zimmermann A., di Sebastiano P., Buechler M.W., Friess H. Ann. Surg. 241:144-151(2005) [PubMed] [Europe PMC] [Abstract] Cited for: TISSUE SPECIFICITY.
[10]	"JMJD6 is a histone arginine demethylase." Chang B., Chen Y., Zhao Y., Bruick R.K. Science 318:444-447(2007) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS HISTONE DEMETHYLASE, MUTAGENESIS OF HIS-187; ASP-189 AND HIS-273.
[11]	"Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing." Webby C.J., Wolf A., Gromak N., Dreger M., Kramer H., Kessler B., Nielsen M.L., Schmitz C., Butler D.S., Yates J.R. III, Delahunty C.M., Hahn P., Lengeling A., Mann M., Proudfoot N.J., Schofield C.J., Boettger A. Science 325:90-93(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION AS LYSYL-HYDROXYLASE, COFACTOR, INTERACTION WITH LUC7L2; LUC7L3 AND U2AF2, MUTAGENESIS OF HIS-187 AND ASP-189.
[12]	"Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation." Hahn P., Wegener I., Burrells A., Bose J., Wolf A., Erck C., Butler D., Schofield C.J., Bottger A., Lengeling A. PLoS ONE 5:E13769-E13769(2010) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION, RNA-BINDING, FUNCTION.
[13]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[14]	"Crystal structure of the 2-oxoglutarate- and Fe(II)-dependent lysyl hydroxylase JMJD6." Mantri M., Krojer T., Bagg E.A., Webby C.J., Butler D.S., Kochan G., Kavanagh K.L., Oppermann U., McDonough M.A., Schofield C.J. J. Mol. Biol. 401:211-222(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 1-335 IN COMPLEX WITH NICKEL IONS, FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TYR-131; LYS-204; GLU-231; THR-285 AND ASN-287.
[15]	"Interaction of JMJD6 with single-stranded RNA." Hong X., Zang J., White J., Wang C., Pan C.H., Zhao R., Murphy R.C., Dai S., Henson P., Kappler J.W., Hagman J., Zhang G. Proc. Natl. Acad. Sci. U.S.A. 107:14568-14572(2010) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS) OF 1-334 IN COMPLEX WITH IRON IONS AND 2-OXOGLUTARATE, POSSIBLE FUNCTION, RNA-BINDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AB073711 mRNA. Translation: BAC16755.1.
AB011157 mRNA. Translation: BAA25511.1. Different initiation.
AK021780 mRNA. Translation: BAG51050.1.
AK294816 mRNA. Translation: BAG57932.1.
AC005837 Genomic DNA. No translation available.
CH471099 Genomic DNA. Translation: EAW89434.1.
BC047003 mRNA. Translation: AAH47003.1. Different initiation.
BC066654 mRNA. Translation: AAH66654.1.

IPI

IPI00375496.
IPI00550958.
IPI00604598.

RefSeq

NP_001074930.1. NM_001081461.1.
NP_055982.2. NM_015167.2.

UniGene

Hs.514505.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3K2O	X-ray	1.75	A/B	1-335	[»]
3LD8	X-ray	2.70	A	1-334	[»]
3LDB	X-ray	2.70	A	1-334	[»]

ProteinModelPortal

Q6NYC1.

ModBase

Search...

Protein-protein interaction databases

STRING

9606.ENSP00000394085.

PTM databases

PhosphoSite

Q6NYC1.

Polymorphism databases

DMDM

67461014.

Proteomic databases

PaxDb

Q6NYC1.

PRIDE

Q6NYC1.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000397625; ENSP00000380750; ENSG00000070495.
ENST00000445478; ENSP00000394085; ENSG00000070495.

GeneID

23210.

KEGG

hsa:23210.

UCSC

uc002jsn.1. human.
uc002jso.3. human.

Organism-specific databases

CTD

23210.

GeneCards

GC17M074708.

HGNC

HGNC:19355. JMJD6.

HPA

CAB004548.

MIM

604914. gene.

neXtProt

NX_Q6NYC1.

PharmGKB

PA162392513.

HUGE

Search...

GenAtlas

Search...

Phylogenomic databases

eggNOG

NOG124833.

HOGENOM

HOG000265824.

HOVERGEN

HBG054774.

InParanoid

Q6NYC1.

KO

K11323.

OMA

MHRRKKR.

OrthoDB

EOG4VMFFJ.

Gene expression databases

ArrayExpress

Q6NYC1.

Bgee

Q6NYC1.

CleanEx

HS_JMJD6.

Genevestigator

Q6NYC1.

GermOnline

ENSG00000070495. Homo sapiens.

Family and domain databases

InterPro

IPR003347. JmjC_dom.
[Graphical view]

Pfam

PF02373. JmjC. 1 hit.
[Graphical view]

SMART

SM00558. JmjC. 1 hit.
[Graphical view]

PROSITE

PS51184. JMJC. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q6NYC1.

GenomeRNAi

23210.

NextBio

44753.

SOURCE

Search...

Entry information

Entry name

JMJD6_HUMAN

Accession

Primary (citable) accession number: Q6NYC1
Secondary accession number(s): B3KMN8 , B4DGX1, Q86VY0, Q8IUM5, Q9Y4E2

Entry history

Integrated into UniProtKB/Swiss-Prot:	June 7, 2005
Last sequence update:	July 5, 2004
Last modified:	May 1, 2013
This is version 92 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.