Reviewed, UniProtKB/Swiss-Prot Q9NQX0 (PRDM6_HUMAN)

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) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › 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.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Chromosomal protein 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
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-KW 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: UniProtKB-KW
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). 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). 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: 10668202] [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: 15372022] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

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.
UniGene	Hs.135118
3D structure databases
ModBase	Search...
Protein-protein interaction databases
STRING	Q9NQX0.
Proteomic databases
PRIDE	Q9NQX0.
Genome annotation databases
Ensembl	ENST00000261364; ENSP00000261364; ENSG00000061455; Homo sapiens. [Genome view] ENST00000407847; ENSP00000384725; ENSG00000061455; Homo sapiens. [Genome view]
GeneID	93166.
KEGG	hsa:93166.
UCSC	uc003kti.1. human.
Organism-specific databases
CTD	93166.
GeneCards	GC05P122452.
HGNC	HGNC:9350. PRDM6.
PharmGKB	PA33718.
GenAtlas	Search...
Phylogenomic databases
eggNOG	prNOG19169.
HOGENOM	HBG506721.
HOVERGEN	Q9NQX0.
InParanoid	Q9NQX0.
OrthoDB	EOG9QC3R8.
Gene expression databases
ArrayExpress	Q9NQX0.
Bgee	Q9NQX0.
CleanEx	HS_PRDM6.
Genevestigator	Q9NQX0.
GermOnline	ENSG00000061455. Homo sapiens.
Family and domain databases
InterPro	IPR001214. SET_dom. IPR007087. Znf_C2H2. IPR015880. Znf_C2H2-like. IPR013087. Znf_C2H2/integrase_DNA-bd. [Graphical view]
Gene3D	G3DSA:3.30.160.60. Znf_C2H2/integrase_DNA-bd. 1 hit.
Pfam	PF00856. SET. 1 hit. PF00096. zf-C2H2. 2 hits. [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...

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:	February 9, 2010
This is version 72 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.