CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015114
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 
Protein Synonyms/Alias
 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 
Gene Name
 JMJD6 
Gene Synonyms/Alias
 KIAA0585; PTDSR 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
68ERYERPYKPVVLLNAubiquitination[1]
100KYRNQKFKCGEDNDGubiquitination[1]
145GEHPKRRKLLEDYKVubiquitination[1]
151RKLLEDYKVPKFFTDubiquitination[1, 2, 3]
167LFQYAGEKRRPPYRWubiquitination[1, 2]
219STPRELIKVTRDEGGubiquitination[1]
Reference
 [1] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [2] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [3] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789] 
Functional Description
 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. 
Sequence Annotation
 DOMAIN 141 305 JmjC.
 MOTIF 6 10 Nuclear localization signal 1.
 MOTIF 91 95 Nuclear localization signal 2.
 MOTIF 141 145 Nuclear localization signal 3.
 MOTIF 167 170 Nuclear localization signal 4.
 MOTIF 373 378 Nuclear localization signal 5.
 METAL 187 187 Iron; catalytic.
 METAL 189 189 Iron; catalytic.
 METAL 273 273 Iron; catalytic.
 BINDING 184 184 Substrate (By similarity).
 BINDING 197 197 2-oxoglutarate.
 BINDING 204 204 Substrate (By similarity).
 BINDING 285 285 2-oxoglutarate.  
Keyword
 3D-structure; 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. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 403 AA 
Protein Sequence
MNHKSKKRIR EAKRSARPEL KDSLDWTRHN YYESFSLSPA AVADNVERAD ALQLSVEEFV 60
ERYERPYKPV VLLNAQEGWS AQEKWTLERL KRKYRNQKFK CGEDNDGYSV KMKMKYYIEY 120
MESTRDDSPL YIFDSSYGEH PKRRKLLEDY KVPKFFTDDL FQYAGEKRRP PYRWFVMGPP 180
RSGTGIHIDP LGTSAWNALV QGHKRWCLFP TSTPRELIKV TRDEGGNQQD EAITWFNVIY 240
PRTQLPTWPP EFKPLEILQK PGETVFVPGG WWHVVLNLDT TIAITQNFAS STNFPVVWHK 300
TVRGRPKLSR KWYRILKQEH PELAVLADSV DLQESTGIAS DSSSDSSSSS SSSSSDSDSE 360
CESGSEGDGT VHRRKKRRTC SMVGNGDTTS QDDCVSKERS SSRIRDTCGG RAHP 414 
Gene Ontology
 GO:0005730; C:nucleolus; IDA:UniProtKB.
 GO:0005654; C:nucleoplasm; IDA:UniProtKB.
 GO:0005886; C:plasma membrane; IEA:Compara.
 GO:0033746; F:histone demethylase activity (H3-R2 specific); IDA:UniProtKB.
 GO:0033749; F:histone demethylase activity (H4-R3 specific); IDA:UniProtKB.
 GO:0042802; F:identical protein binding; IDA:BHF-UCL.
 GO:0005506; F:iron ion binding; IDA:UniProtKB.
 GO:0016702; F:oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen; IEA:UniProtKB-KW.
 GO:0070815; F:peptidyl-lysine 5-dioxygenase activity; IDA:UniProtKB.
 GO:0004872; F:receptor activity; IEA:Compara.
 GO:0003727; F:single-stranded RNA binding; IDA:UniProtKB.
 GO:0006915; P:apoptotic process; IEA:Compara.
 GO:0007166; P:cell surface receptor signaling pathway; IEA:Compara.
 GO:0048821; P:erythrocyte development; IEA:Compara.
 GO:0007507; P:heart development; IEA:Compara.
 GO:0001822; P:kidney development; IEA:Compara.
 GO:0030324; P:lung development; IEA:Compara.
 GO:0042116; P:macrophage activation; IEA:Compara.
 GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
 GO:0018395; P:peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; IDA:UniProtKB.
 GO:0043654; P:recognition of apoptotic cell; IEA:Compara.
 GO:0048024; P:regulation of mRNA splicing, via spliceosome; IMP:UniProtKB.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0060041; P:retina development in camera-type eye; IEA:Compara.
 GO:0008380; P:RNA splicing; IEA:UniProtKB-KW.
 GO:0002040; P:sprouting angiogenesis; ISS:UniProtKB.
 GO:0033077; P:T cell differentiation in thymus; IEA:Compara.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR003347; JmjC_dom. 
Pfam
 PF02373; JmjC 
SMART
 SM00558; JmjC 
PROSITE
 PS51184; JMJC 
PRINTS