Q9NQX0 (PRDM6_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Putative histone-lysine N-methyltransferase PRDM6
EC=2.1.1.43

Alternative name(s):
PR domain zinc finger protein 6
PR domain-containing protein 6

Gene names

Name:	PRDM6
Synonyms:	PFM3

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	595 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it possesses histone methyltransferase activity when associated with other proteins and specifically methylates 'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional repression By similarity.
Catalytic activity	S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].
Subunit structure	Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300 By similarity.
Subcellular location	Nucleus By similarity.
Sequence similarities	Contains 4 C2H2-type zinc fingers. Contains 1 SET domain.
Sequence caution	The sequence AAF78078.1 differs from that shown. Reason: Erroneous initiation. The sequence AAF78079.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Coding sequence diversity	Alternative splicing
Domain	Repeat Zinc-finger
Ligand	Metal-binding S-adenosyl-L-methionine Zinc
Molecular function	Chromatin regulator Methyltransferase Repressor Transferase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone lysine methylation Inferred from electronic annotation. Source: GOC negative regulation of smooth muscle cell differentiation Inferred from electronic annotation. Source: Compara negative regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: Compara neurogenesis Inferred from electronic annotation. Source: Compara transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	histone-lysine N-methyltransferase activity Inferred from electronic annotation. Source: EC nucleic acid binding Inferred from electronic annotation. Source: InterPro zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Alternative products

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

Isoform 1 (identifier: Q9NQX0-3)

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: Q9NQX0-2)

Also known as: B;

The sequence of this isoform differs from the canonical sequence as follows:
     1-182: Missing.
     314-595: Missing.

Isoform 3 (identifier: Q9NQX0-1)

Also known as: A;

The sequence of this isoform differs from the canonical sequence as follows:
     1-182: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 595	595	Putative histone-lysine N-methyltransferase PRDM6		PRO_0000047762
Regions
	Domain	247 – 369	123	SET
	Zinc finger	473 – 495	23	C2H2-type 1; degenerate
	Zinc finger	501 – 523	23	C2H2-type 2
	Zinc finger	529 – 551	23	C2H2-type 3
	Zinc finger	557 – 579	23	C2H2-type 4; degenerate
	Compositional bias	47 – 73	27	Pro-rich
	Compositional bias	97 – 106	10	Poly-Ala
	Compositional bias	123 – 129	7	Poly-Ala
	Compositional bias	151 – 162	12	Poly-Gly
	Compositional bias	228 – 232	5	Poly-Ala
Natural variations
	Alternative sequence	1 – 182	182	Missing in isoform 2 and isoform 3.		VSP_036348
	Alternative sequence	314 – 595	282	Missing in isoform 2.		VSP_006929

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified February 10, 2009. Version 2. Checksum: DB8D815E7C107451	FASTA	595	64,452
	10 20 30 40 50 60 MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GAGPLKGSGA AGLLSAPQPL QPPPPPPPPE 70 80 90 100 110 120 RAEPPPDSLR PRPASLSSAS STPASSSTSA SSASSCAAAA AAAALAGLSA LPVSQLPVFA 130 140 150 160 170 180 PLAAAAVAAE PLPPKELCLG ATSGPGPVKC GGGGGGGGEG RGAPRFRCSA EELDYYLYGQ 190 200 210 220 230 240 QRMEIIPLNQ HTSDPNNRCD MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW 250 260 270 280 290 300 LRDLPREVCL CTSTVPGLAY GICAAQRIQQ GTWIGPFQGV LLPPEKVQAG AVRNTQHLWE 310 320 330 340 350 360 IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA CIDIPRGTEL 370 380 390 400 410 420 LVWYNDSYTS FFGIPLQCIA QDENLNVPST VMEAMCRQDA LQPFNKSSKL APTTQQRSVV 430 440 450 460 470 480 FPQTPCSRNF SLLDKSGPIE SGFNQINVKN QRVLASPTST SQLHSEFSDW HLWKCGQCFK 490 500 510 520 530 540 TFTQRILLQM HVCTQNPDRP YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG 550 560 570 580 590 ATTLNNHIRT HTGEKPFKCE RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD
	Isoform 2 (B) [UniParc]. Checksum: 1C608683110D5DC2	FASTA	131	14,436
	10 20 30 40 50 60 MEIIPLNQHT SDPNNRCDMC ADNRNGECPM HGPLHSLRRL VGTSSAAAAA PPPELPEWLR 70 80 90 100 110 120 DLPREVCLCT STVPGLAYGI CAAQRIQQGT WIGPFQGVLL PPEKVQAGAV RNTQHLWEIY 130 DQDGTLQHFI D
	Isoform 3 (A) [UniParc]. Checksum: 9D5FCB5B9F885666	FASTA	413	46,635
	10 20 30 40 50 60 MEIIPLNQHT SDPNNRCDMC ADNRNGECPM HGPLHSLRRL VGTSSAAAAA PPPELPEWLR 70 80 90 100 110 120 DLPREVCLCT STVPGLAYGI CAAQRIQQGT WIGPFQGVLL PPEKVQAGAV RNTQHLWEIY 130 140 150 160 170 180 DQDGTLQHFI DGGEPSKSSW MRYIRCARHC GEQNLTVVQY RSNIFYRACI DIPRGTELLV 190 200 210 220 230 240 WYNDSYTSFF GIPLQCIAQD ENLNVPSTVM EAMCRQDALQ PFNKSSKLAP TTQQRSVVFP 250 260 270 280 290 300 QTPCSRNFSL LDKSGPIESG FNQINVKNQR VLASPTSTSQ LHSEFSDWHL WKCGQCFKTF 310 320 330 340 350 360 TQRILLQMHV CTQNPDRPYQ CGHCSQSFSQ PSELRNHVVT HSSDRPFKCG YCGRAFAGAT 370 380 390 400 410 TLNNHIRTHT GEKPFKCERC ERSFTQATQL SRHQRMPNEC KPITESPESI EVD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The yin-yang of PR-domain family genes in tumorigenesis." Jiang G.L., Huang S. Histol. Histopathol. 15:109-117(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 2 AND 3).
[2]	"The DNA sequence and comparative analysis of human chromosome 5." Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S. , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M. Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF272898 mRNA. Translation: AAF78078.1. Different initiation. AF272899 mRNA. Translation: AAF78079.1. Different initiation. AC008548 Genomic DNA. No translation available. AC106786 Genomic DNA. No translation available.
IPI	IPI00218376. IPI00248395. IPI00921397.
RefSeq	NP_001129711.1. NM_001136239.1.
UniGene	Hs.135118.
3D structure databases
ProteinModelPortal	Q9NQX0.
ModBase	Search...
PTM databases
PhosphoSite	Q9NQX0.
Polymorphism databases
DMDM	223590133.
Proteomic databases
PaxDb	Q9NQX0.
PRIDE	Q9NQX0.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENST00000407847; ENSP00000384725; ENSG00000061455.
GeneID	93166.
KEGG	hsa:93166.
UCSC	uc003kti.3. human.
Organism-specific databases
CTD	93166.
GeneCards	GC05P122424.
HGNC	HGNC:9350. PRDM6.
HPA	HPA030322. HPA030324.
neXtProt	NX_Q9NQX0.
PharmGKB	PA33718.
GenAtlas	Search...
Phylogenomic databases
eggNOG	NOG325470.
HOGENOM	HOG000090218.
HOVERGEN	HBG108289.
InParanoid	Q9NQX0.
OMA	MESGFNQ.
OrthoDB	EOG4TQM8R.
Gene expression databases
Bgee	Q9NQX0.
CleanEx	HS_PRDM6.
Genevestigator	Q9NQX0.
GermOnline	ENSG00000061455. Homo sapiens.
Family and domain databases
Gene3D	3.30.160.60. 3 hits.
InterPro	IPR001214. SET_dom. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Pfam	PF00856. SET. 1 hit. PF00096. zf-C2H2. 1 hit. [Graphical view]
SMART	SM00317. SET. 1 hit. SM00355. ZnF_C2H2. 4 hits. [Graphical view]
PROSITE	PS50280. SET. 1 hit. PS00028. ZINC_FINGER_C2H2_1. 2 hits. PS50157. ZINC_FINGER_C2H2_2. 4 hits. [Graphical view]
ProtoNet	Search...
Other
GenomeRNAi	93166.
NextBio	78013.

Entry information

Entry name

PRDM6_HUMAN

Accession

Primary (citable) accession number: Q9NQX0
Secondary accession number(s): B5MCJ4, Q9NQW9

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 8, 2002
Last sequence update:	February 10, 2009
Last modified:	May 1, 2013
This is version 104 of the entry and version 2 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.