GenomeNet

Database: UniProt
Entry: Q9NQX0
LinkDB: Q9NQX0
Original site: Q9NQX0 
ID   PRDM6_HUMAN             Reviewed;         595 AA.
AC   Q9NQX0; B5MCJ4; Q9NQW9;
DT   08-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT   10-FEB-2009, sequence version 2.
DT   13-FEB-2019, entry version 156.
DE   RecName: Full=Putative histone-lysine N-methyltransferase PRDM6;
DE            EC=2.1.1.43;
DE   AltName: Full=PR domain zinc finger protein 6;
DE   AltName: Full=PR domain-containing protein 6;
GN   Name=PRDM6; Synonyms=PFM3;
OS   Homo sapiens (Human).
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC   Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
OC   Catarrhini; Hominidae; Homo.
OX   NCBI_TaxID=9606;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
RX   PubMed=10668202;
RA   Jiang G.L., Huang S.;
RT   "The yin-yang of PR-domain family genes in tumorigenesis.";
RL   Histol. Histopathol. 15:109-117(2000).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=15372022; DOI=10.1038/nature02919;
RA   Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S.,
RA   Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M.,
RA   She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S.,
RA   Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M.,
RA   Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T.,
RA   Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M.,
RA   Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K.,
RA   Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C.,
RA   Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M.,
RA   Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A.,
RA   Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M.,
RA   Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M.,
RA   Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S.,
RA   Richardson P., Lucas S.M., Myers R.M., Rubin E.M.;
RT   "The DNA sequence and comparative analysis of human chromosome 5.";
RL   Nature 431:268-274(2004).
RN   [3]
RP   INVOLVEMENT IN PDA3, AND VARIANTS PDA3 SER-263; ARG-462 AND GLN-549.
RX   PubMed=27181681; DOI=10.1016/j.ajhg.2016.03.022;
RA   Li N., Subrahmanyan L., Smith E., Yu X., Zaidi S., Choi M., Mane S.,
RA   Nelson-Williams C., Bahjati M., Kazemi M., Hashemi M., Fathzadeh M.,
RA   Narayanan A., Tian L., Montazeri F., Mani M., Begleiter M.L.,
RA   Coon B.G., Lynch H.T., Olson E.N., Zhao H., Ruland J., Lifton R.P.,
RA   Mani A.;
RT   "Mutations in the histone modifier PRDM6 are associated with isolated
RT   nonsyndromic patent ductus arteriosus.";
RL   Am. J. Hum. Genet. 98:1082-1091(2016).
CC   -!- FUNCTION: Putative histone methyltransferase that acts as a
CC       transcriptional repressor of smooth muscle gene expression.
CC       Promotes the transition from differentiated to proliferative
CC       smooth muscle by suppressing differentiation and maintaining the
CC       proliferative potential of vascular smooth muscle cells. Also
CC       plays a role in endothelial cells by inhibiting endothelial cell
CC       proliferation, survival and differentiation. It is unclear whether
CC       it has histone methyltransferase activity in vivo. According to
CC       some authors, it does not act as a histone methyltransferase by
CC       itself and represses transcription by recruiting EHMT2/G9a.
CC       According to others, it possesses histone methyltransferase
CC       activity when associated with other proteins and specifically
CC       methylates 'Lys-20' of histone H4 in vitro. 'Lys-20' methylation
CC       represents a specific tag for epigenetic transcriptional
CC       repression. {ECO:0000250|UniProtKB:Q3UZD5}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) +
CC         N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine;
CC         Xref=Rhea:RHEA:10024, Rhea:RHEA-COMP:9845, Rhea:RHEA-COMP:9846,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29969, ChEBI:CHEBI:57856,
CC         ChEBI:CHEBI:59789, ChEBI:CHEBI:61929; EC=2.1.1.43;
CC   -!- SUBUNIT: Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.
CC       {ECO:0000250|UniProtKB:Q3UZD5}.
CC   -!- INTERACTION:
CC       Q9NYB9-2:ABI2; NbExp=4; IntAct=EBI-11320284, EBI-11096309;
CC       O43865:AHCYL1; NbExp=4; IntAct=EBI-11320284, EBI-2371423;
CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q3UZD5}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q9NQX0-3; Sequence=Displayed;
CC       Name=2; Synonyms=B;
CC         IsoId=Q9NQX0-2; Sequence=VSP_036348, VSP_006929;
CC       Name=3; Synonyms=A;
CC         IsoId=Q9NQX0-1; Sequence=VSP_036348;
CC   -!- DISEASE: Patent ductus arteriosus 3 (PDA3) [MIM:617039]: A
CC       congenital heart defect characterized by the persistent opening of
CC       fetal ductus arteriosus that fails to close after birth. Fetal
CC       ductus arteriosus connects the pulmonary artery to the descending
CC       aorta, allowing unoxygenated blood to bypass the lung and flow to
CC       the placenta. Normally, the ductus occludes shortly after birth.
CC       {ECO:0000269|PubMed:27181681}. Note=The disease is caused by
CC       mutations affecting the gene represented in this entry.
CC   -!- SIMILARITY: Belongs to the class V-like SAM-binding
CC       methyltransferase superfamily. {ECO:0000255|PROSITE-
CC       ProRule:PRU00190}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF78078.1; Type=Erroneous initiation; Evidence={ECO:0000305};
CC       Sequence=AAF78079.1; Type=Erroneous initiation; Evidence={ECO:0000305};
DR   EMBL; AF272898; AAF78078.1; ALT_INIT; mRNA.
DR   EMBL; AF272899; AAF78079.1; ALT_INIT; mRNA.
DR   EMBL; AC008548; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; AC106786; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   CCDS; CCDS47259.1; -. [Q9NQX0-3]
DR   RefSeq; NP_001129711.1; NM_001136239.1. [Q9NQX0-3]
DR   UniGene; Hs.135118; -.
DR   ProteinModelPortal; Q9NQX0; -.
DR   BioGrid; 125009; 12.
DR   IntAct; Q9NQX0; 70.
DR   MINT; Q9NQX0; -.
DR   STRING; 9606.ENSP00000384725; -.
DR   iPTMnet; Q9NQX0; -.
DR   PhosphoSitePlus; Q9NQX0; -.
DR   BioMuta; PRDM6; -.
DR   DMDM; 223590133; -.
DR   jPOST; Q9NQX0; -.
DR   PaxDb; Q9NQX0; -.
DR   PeptideAtlas; Q9NQX0; -.
DR   PRIDE; Q9NQX0; -.
DR   ProteomicsDB; 82215; -.
DR   ProteomicsDB; 82216; -. [Q9NQX0-1]
DR   ProteomicsDB; 82217; -. [Q9NQX0-2]
DR   Ensembl; ENST00000407847; ENSP00000384725; ENSG00000061455. [Q9NQX0-3]
DR   GeneID; 93166; -.
DR   KEGG; hsa:93166; -.
DR   UCSC; uc003kti.4; human. [Q9NQX0-3]
DR   CTD; 93166; -.
DR   DisGeNET; 93166; -.
DR   EuPathDB; HostDB:ENSG00000061455.10; -.
DR   GeneCards; PRDM6; -.
DR   HGNC; HGNC:9350; PRDM6.
DR   HPA; HPA030322; -.
DR   HPA; HPA030324; -.
DR   MalaCards; PRDM6; -.
DR   MIM; 616982; gene.
DR   MIM; 617039; phenotype.
DR   neXtProt; NX_Q9NQX0; -.
DR   OpenTargets; ENSG00000061455; -.
DR   Orphanet; 466729; Familial patent arterial duct.
DR   PharmGKB; PA33718; -.
DR   eggNOG; KOG1721; Eukaryota.
DR   eggNOG; KOG2461; Eukaryota.
DR   eggNOG; ENOG410XRVC; LUCA.
DR   GeneTree; ENSGT00940000155852; -.
DR   HOGENOM; HOG000090218; -.
DR   HOVERGEN; HBG108289; -.
DR   InParanoid; Q9NQX0; -.
DR   KO; K20795; -.
DR   OMA; PPEIPEW; -.
DR   OrthoDB; 1318335at2759; -.
DR   PhylomeDB; Q9NQX0; -.
DR   TreeFam; TF106403; -.
DR   GenomeRNAi; 93166; -.
DR   PRO; PR:Q9NQX0; -.
DR   Proteomes; UP000005640; Chromosome 5.
DR   Bgee; ENSG00000061455; Expressed in 126 organ(s), highest expression level in descending thoracic aorta.
DR   ExpressionAtlas; Q9NQX0; baseline and differential.
DR   Genevisible; Q9NQX0; HS.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0031490; F:chromatin DNA binding; IBA:GO_Central.
DR   GO; GO:0003700; F:DNA-binding transcription factor activity; IBA:GO_Central.
DR   GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; ISA:NTNU_SB.
DR   GO; GO:0018024; F:histone-lysine N-methyltransferase activity; IEA:UniProtKB-EC.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0042803; F:protein homodimerization activity; IEA:Ensembl.
DR   GO; GO:0000977; F:RNA polymerase II regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0043565; F:sequence-specific DNA binding; IBA:GO_Central.
DR   GO; GO:0051151; P:negative regulation of smooth muscle cell differentiation; IEA:Ensembl.
DR   GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IBA:GO_Central.
DR   GO; GO:0022008; P:neurogenesis; IBA:GO_Central.
DR   InterPro; IPR001214; SET_dom.
DR   InterPro; IPR036236; Znf_C2H2_sf.
DR   InterPro; IPR013087; Znf_C2H2_type.
DR   Pfam; PF00856; SET; 1.
DR   Pfam; PF00096; zf-C2H2; 3.
DR   SMART; SM00317; SET; 1.
DR   SMART; SM00355; ZnF_C2H2; 4.
DR   SUPFAM; SSF57667; SSF57667; 2.
DR   PROSITE; PS50280; SET; 1.
DR   PROSITE; PS00028; ZINC_FINGER_C2H2_1; 2.
DR   PROSITE; PS50157; ZINC_FINGER_C2H2_2; 4.
PE   1: Evidence at protein level;
KW   Alternative splicing; Chromatin regulator; Complete proteome;
KW   Disease mutation; Metal-binding; Methyltransferase; Nucleus;
KW   Polymorphism; Reference proteome; Repeat; Repressor;
KW   S-adenosyl-L-methionine; Transcription; Transcription regulation;
KW   Transferase; Zinc; Zinc-finger.
FT   CHAIN         1    595       Putative histone-lysine N-
FT                                methyltransferase PRDM6.
FT                                /FTId=PRO_0000047762.
FT   DOMAIN      246    365       SET. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00190}.
FT   ZN_FING     473    495       C2H2-type 1; degenerate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00042}.
FT   ZN_FING     501    523       C2H2-type 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     529    551       C2H2-type 3. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00042}.
FT   ZN_FING     557    579       C2H2-type 4; degenerate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00042}.
FT   COMPBIAS     47     73       Pro-rich.
FT   COMPBIAS     97    106       Poly-Ala.
FT   COMPBIAS    123    129       Poly-Ala.
FT   COMPBIAS    151    162       Poly-Gly.
FT   COMPBIAS    228    232       Poly-Ala.
FT   VAR_SEQ       1    182       Missing (in isoform 2 and isoform 3).
FT                                {ECO:0000303|PubMed:10668202}.
FT                                /FTId=VSP_036348.
FT   VAR_SEQ     314    595       Missing (in isoform 2).
FT                                {ECO:0000303|PubMed:10668202}.
FT                                /FTId=VSP_006929.
FT   VARIANT     263    263       C -> S (in PDA3; unknown pathological
FT                                significance; dbSNP:rs879255279).
FT                                {ECO:0000269|PubMed:27181681}.
FT                                /FTId=VAR_077014.
FT   VARIANT     462    462       Q -> R (in PDA3; dbSNP:rs879253872).
FT                                {ECO:0000269|PubMed:27181681}.
FT                                /FTId=VAR_077015.
FT   VARIANT     549    549       R -> Q (in PDA3; dbSNP:rs879255278).
FT                                {ECO:0000269|PubMed:27181681}.
FT                                /FTId=VAR_077016.
SQ   SEQUENCE   595 AA;  64452 MW;  DB8D815E7C107451 CRC64;
     MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GAGPLKGSGA AGLLSAPQPL QPPPPPPPPE
     RAEPPPDSLR PRPASLSSAS STPASSSTSA SSASSCAAAA AAAALAGLSA LPVSQLPVFA
     PLAAAAVAAE PLPPKELCLG ATSGPGPVKC GGGGGGGGEG RGAPRFRCSA EELDYYLYGQ
     QRMEIIPLNQ HTSDPNNRCD MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW
     LRDLPREVCL CTSTVPGLAY GICAAQRIQQ GTWIGPFQGV LLPPEKVQAG AVRNTQHLWE
     IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA CIDIPRGTEL
     LVWYNDSYTS FFGIPLQCIA QDENLNVPST VMEAMCRQDA LQPFNKSSKL APTTQQRSVV
     FPQTPCSRNF SLLDKSGPIE SGFNQINVKN QRVLASPTST SQLHSEFSDW HLWKCGQCFK
     TFTQRILLQM HVCTQNPDRP YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG
     ATTLNNHIRT HTGEKPFKCE RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD
//
DBGET integrated database retrieval system