Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

Gene

JMJD6

Organism
Bos taurus (Bovine)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript leveli

Functioni

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).By similarity

Cofactori

Fe2+By similarityNote: Binds 1 Fe2+ ion per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei184 – 1841SubstrateBy similarity
Metal bindingi187 – 1871Iron; catalyticPROSITE-ProRule annotation
Metal bindingi189 – 1891Iron; catalyticPROSITE-ProRule annotation
Binding sitei197 – 19712-oxoglutarateBy similarity
Binding sitei204 – 2041SubstrateBy similarity
Metal bindingi273 – 2731Iron; catalyticPROSITE-ProRule annotation
Binding sitei285 – 28512-oxoglutarateBy similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Developmental protein, Dioxygenase, Oxidoreductase

Keywords - Biological processi

Differentiation, mRNA processing, mRNA splicing, Transcription, Transcription regulation

Keywords - Ligandi

Iron, Metal-binding, RNA-binding

Enzyme and pathway databases

ReactomeiR-BTA-3214842. HDMs demethylate histones.

Names & Taxonomyi

Protein namesi
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 namesi
Name:JMJD6By similarity
Synonyms:PTDSRImported
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Chromosome 19

Subcellular locationi

  • Nucleusnucleoplasm By similarity
  • Nucleusnucleolus 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).By similarity

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 403403Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6PRO_0000312839Add
BLAST

Proteomic databases

PaxDbiQ58DS6.
PRIDEiQ58DS6.

Interactioni

Subunit structurei

Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65. Interacts with BRD4 (By similarity).Interacts with LIAT1 (By similarity).By similarity

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000025492.

Structurei

3D structure databases

ProteinModelPortaliQ58DS6.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini141 – 305165JmjCPROSITE-ProRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi6 – 105Nuclear localization signal 1By similarity
Motifi91 – 955Nuclear localization signal 2By similarity
Motifi141 – 1455Nuclear localization signal 3By similarity
Motifi167 – 1704Nuclear localization signal 4By similarity
Motifi373 – 3786Nuclear localization signal 5By similarity

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi340 – 36526Ser-richSequence analysisAdd
BLAST

Domaini

The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus.By similarity

Sequence similaritiesi

Belongs to the JMJD6 family.Curated
Contains 1 JmjC domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiKOG2130. Eukaryota.
ENOG410XQCR. LUCA.
GeneTreeiENSGT00530000063579.
HOGENOMiHOG000265824.
HOVERGENiHBG054774.
InParanoidiQ58DS6.
KOiK11323.
OMAiGMMHRRK.
OrthoDBiEOG7R56SG.
TreeFamiTF314988.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q58DS6-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YFESFPLNPA AVADNVERAD
60 70 80 90 100
ALQLSVEEFV ERYERPYKPV VLLNAQEGWS AQEKWTLERL KRKYRNQKFK
110 120 130 140 150
CGEDNDGYSV KMKMKYYIEY MESTRDDSPL YIFDSSYGEH PKRRKLLEDY
160 170 180 190 200
KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP RSGTGIHIDP LGTSAWNALV
210 220 230 240 250
QGHKRWCLFP TSTPRELIKV TREEGGNQQD EAITWFNIIY PRTQLPTWPP
260 270 280 290 300
EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK
310 320 330 340 350
TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS
360 370 380 390 400
SSSSSDSDSE CESGSEGEGT MHRRKKRRTC GMVGNGDTTS QDDCVSKERS

SSR
Length:403
Mass (Da):46,527
Last modified:April 26, 2005 - v1
Checksum:i74BC887C072B3A59
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT021521 mRNA. Translation: AAX46368.1.
RefSeqiNP_001029492.2. NM_001034320.2.
UniGeneiBt.32358.

Genome annotation databases

EnsembliENSBTAT00000025492; ENSBTAP00000025492; ENSBTAG00000019153.
GeneIDi508343.
KEGGibta:508343.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BT021521 mRNA. Translation: AAX46368.1.
RefSeqiNP_001029492.2. NM_001034320.2.
UniGeneiBt.32358.

3D structure databases

ProteinModelPortaliQ58DS6.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000025492.

Proteomic databases

PaxDbiQ58DS6.
PRIDEiQ58DS6.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSBTAT00000025492; ENSBTAP00000025492; ENSBTAG00000019153.
GeneIDi508343.
KEGGibta:508343.

Organism-specific databases

CTDi23210.

Phylogenomic databases

eggNOGiKOG2130. Eukaryota.
ENOG410XQCR. LUCA.
GeneTreeiENSGT00530000063579.
HOGENOMiHOG000265824.
HOVERGENiHBG054774.
InParanoidiQ58DS6.
KOiK11323.
OMAiGMMHRRK.
OrthoDBiEOG7R56SG.
TreeFamiTF314988.

Enzyme and pathway databases

ReactomeiR-BTA-3214842. HDMs demethylate histones.

Miscellaneous databases

NextBioi20868470.

Family and domain databases

InterProiIPR003347. JmjC_dom.
[Graphical view]
PfamiPF02373. JmjC. 1 hit.
[Graphical view]
SMARTiSM00558. JmjC. 1 hit.
[Graphical view]
PROSITEiPS51184. JMJC. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiJMJD6_BOVIN
AccessioniPrimary (citable) accession number: Q58DS6
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: April 26, 2005
Last modified: February 17, 2016
This is version 68 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.