Reviewed, UniProtKB/Swiss-Prot Q3UZD5 (PRDM6_MOUSE)

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
    PR domain-containing protein in smooth muscle

Gene names

Name:	Prdm6
Synonyms:	Gm92, Prism

Organism

Mus musculus (Mouse)

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus

Protein attributes

Sequence length	596 AA.
Sequence status	Complete.
Protein existence	Evidence at protein 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 Ref.1, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to Ref.4, 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. Ref.1 Ref.4
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. Ref.1
Subcellular location	Nucleus Ref.1 Ref.4.
Tissue specificity	Expressed in a variety of smooth muscle-containing tissues and displays especially robust expression in the cardiac outflow tract and descending aorta during embryogenesis. Also enriched in vascular precursors during development. Ref.1 Ref.4
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
Gene Ontology (GO)
Biological process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of smooth muscle cell differentiation Ref.1 Inferred from mutant phenotype. Source: MGI negative regulation of transcription Ref.1 Inferred from direct assay. Source: MGI neurogenesis Inferred from direct assay. Source: MGI transcription Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	chromosome Inferred from electronic annotation. Source: UniProtKB-KW nucleus Ref.1 Inferred from direct assay. Source: MGI
Molecular function	histone-lysine N-methyltransferase activity Inferred from electronic annotation. Source: EC nucleic acid binding Inferred from electronic annotation. Source: InterPro protein homodimerization activity Ref.1 Inferred from direct assay. Source: MGI zinc ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: Q3UZD5-1)

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: Q3UZD5-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-201: Missing.

Isoform 3 (identifier: Q3UZD5-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-392: Missing.

Isoform 4 (identifier: Q3UZD5-4)

The sequence of this isoform differs from the canonical sequence as follows:
     28-58: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 596	596	Putative histone-lysine N-methyltransferase PRDM6		PRO_0000363959
Regions
	Domain	248 – 370	123	SET
	Zinc finger	474 – 496	23	C2H2-type 1; degenerate
	Zinc finger	502 – 524	23	C2H2-type 2
	Zinc finger	530 – 552	23	C2H2-type 3
	Zinc finger	558 – 580	23	C2H2-type 4; degenerate
	Compositional bias	30 – 35	6	Poly-Gly
	Compositional bias	49 – 86	38	Pro-rich
	Compositional bias	98 – 107	10	Poly-Ala
	Compositional bias	124 – 130	7	Poly-Ala
	Compositional bias	152 – 156	5	Poly-Gly
	Compositional bias	229 – 233	5	Poly-Ala
Natural variations
	Alternative sequence	1 – 392	392	Missing in isoform 3.		VSP_036372
	Alternative sequence	1 – 201	201	Missing in isoform 2.		VSP_036371
	Alternative sequence	28 – 58	31	Missing in isoform 4.		VSP_036373

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified October 11, 2005. Version 1. Checksum: 1DEDC155893CC809	FASTA	596	64,503
	10 20 30 40 50 60 MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GGGGGPLKAS GAALALGAPQ PLQPPPPPPP 70 80 90 100 110 120 PPPERAEPPP DGLRPRPASL SSTPAPSSTS ASSASSCAAA AAAAALAGLS ALPVAQMPVF 130 140 150 160 170 180 APLAAAAVAA EPLPPKDLCL GASAGPGPAK CGGGGGSVGD GRGVPRFRCS AEELDYYLYG 190 200 210 220 230 240 QQRMEIIPLN QHTSDPNNRC DMCADNRNGE CPMHGPLHSL RRLVGTSSAA AAAPPPELPE 250 260 270 280 290 300 WLRDLPREVC LCTSTVPGLA YGICAAQRIQ QGTWIGPFQG VLLSPEKVQT GVVRNTQHLW 310 320 330 340 350 360 EIYDQDGTLQ HFIDGGEPSK SSWMRYIRCA RHCGEQNLTV VQYRSNIFYR ACIDIPRGTE 370 380 390 400 410 420 LLVWYNDSYT SFFGIPLQCI AQDENLNVPS TVMEAMCRQD ALQPFNKSSK LSPSGQQRSV 430 440 450 460 470 480 VFPQTPCSRN FSLLDKSGPM EAGFNQINVK NQRVLASPTS TSQLHSEFSD WHLWKCGQCF 490 500 510 520 530 540 KTFTQRILLQ MHVCTQNPDR PYQCGHCSQS FSQPSELRNH VVTHSSDRPF KCGYCGRAFA 550 560 570 580 590 GATTLNNHIR THTGEKPFKC ERCERSFTQA TQLSRHQRMP NECKPITESP ESIEVD
	Isoform 2. Checksum: E5783499DAC230D5	FASTA	395	44,563
	10 20 30 40 50 60 MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW LRDLPREVCL CTSTVPGLAY 70 80 90 100 110 120 GICAAQRIQQ GTWIGPFQGV LLSPEKVQTG VVRNTQHLWE IYDQDGTLQH FIDGGEPSKS 130 140 150 160 170 180 SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA CIDIPRGTEL LVWYNDSYTS FFGIPLQCIA 190 200 210 220 230 240 QDENLNVPST VMEAMCRQDA LQPFNKSSKL SPSGQQRSVV FPQTPCSRNF SLLDKSGPME 250 260 270 280 290 300 AGFNQINVKN QRVLASPTST SQLHSEFSDW HLWKCGQCFK TFTQRILLQM HVCTQNPDRP 310 320 330 340 350 360 YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG ATTLNNHIRT HTGEKPFKCE 370 380 390 RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD
	Isoform 3. Checksum: 5C0F29D2DBBCC701	FASTA	204	23,214
	10 20 30 40 50 60 MEAMCRQDAL QPFNKSSKLS PSGQQRSVVF PQTPCSRNFS LLDKSGPMEA GFNQINVKNQ 70 80 90 100 110 120 RVLASPTSTS QLHSEFSDWH LWKCGQCFKT FTQRILLQMH VCTQNPDRPY QCGHCSQSFS 130 140 150 160 170 180 QPSELRNHVV THSSDRPFKC GYCGRAFAGA TTLNNHIRTH TGEKPFKCER CERSFTQATQ 190 200 LSRHQRMPNE CKPITESPES IEVD
	Isoform 4. Checksum: 680CC5ADB3468C1D	FASTA	565	61,756
	10 20 30 40 50 60 MLKPGDPGGS AFLKVDPAYL QHWQQLFPPP PPERAEPPPD GLRPRPASLS STPAPSSTSA 70 80 90 100 110 120 SSASSCAAAA AAAALAGLSA LPVAQMPVFA PLAAAAVAAE PLPPKDLCLG ASAGPGPAKC 130 140 150 160 170 180 GGGGGSVGDG RGVPRFRCSA EELDYYLYGQ QRMEIIPLNQ HTSDPNNRCD MCADNRNGEC 190 200 210 220 230 240 PMHGPLHSLR RLVGTSSAAA AAPPPELPEW LRDLPREVCL CTSTVPGLAY GICAAQRIQQ 250 260 270 280 290 300 GTWIGPFQGV LLSPEKVQTG VVRNTQHLWE IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR 310 320 330 340 350 360 HCGEQNLTVV QYRSNIFYRA CIDIPRGTEL LVWYNDSYTS FFGIPLQCIA QDENLNVPST 370 380 390 400 410 420 VMEAMCRQDA LQPFNKSSKL SPSGQQRSVV FPQTPCSRNF SLLDKSGPME AGFNQINVKN 430 440 450 460 470 480 QRVLASPTST SQLHSEFSDW HLWKCGQCFK TFTQRILLQM HVCTQNPDRP YQCGHCSQSF 490 500 510 520 530 540 SQPSELRNHV VTHSSDRPFK CGYCGRAFAG ATTLNNHIRT HTGEKPFKCE RCERSFTQAT 550 560 QLSRHQRMPN ECKPITESPE SIEVD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"PRISM/PRDM6, a transcriptional repressor that promotes the proliferative gene program in smooth muscle cells." Davis C.A., Haberland M., Arnold M.A., Sutherland L.B., McDonald O.G., Richardson J.A., Childs G., Harris S., Owens G.K., Olson E.N. Mol. Cell. Biol. 26:2626-2636(2006) [PubMed: 16537907] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), NUCLEOTIDE SEQUENCE [MRNA] OF 162-596 (ISOFORM 1), FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, INTERACTION WITH HDAC1; HDAC2; HDAC3; CBX1 AND EP300.
[2]	"The transcriptional landscape of the mammalian genome." Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J. , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y. Science 309:1559-1563(2005) [PubMed: 16141072] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 3). Strain: C57BL/6J. Tissue: Egg.
[3]	"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)." The MGC Project Team Genome Res. 14:2121-2127(2004) [PubMed: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: Brain.
[4]	"PRDM6 is enriched in vascular precursors during development and inhibits endothelial cell proliferation, survival, and differentiation." Wu Y., Ferguson J.E. III, Wang H., Kelley R., Ren R., McDonough H., Meeker J., Charles P.C., Wang H., Patterson C. J. Mol. Cell. Cardiol. 44:47-58(2008) [PubMed: 17662997] [Abstract] Cited for: FUNCTION, ALTERNATIVE SPLICING (ISOFORM 4), SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	DQ340564 mRNA. Translation: ABC69307.1. DQ340565 mRNA. Translation: ABC69308.1. AK133910 mRNA. Translation: BAE21922.1. AK135836 mRNA. Translation: BAE22684.1. AK135840 mRNA. Translation: BAE22688.1. BC139295 mRNA. Translation: AAI39296.1.
IPI	IPI00115111. IPI00776371. IPI00855029. IPI00921644.
RefSeq	NP_001028453.1.
UniGene	Mm.297645
3D structure databases
SMR	Q3UZD5. Positions 244-378, 470-579.
ModBase	Search...
Protein-protein interaction databases
STRING	Q3UZD5.
Proteomic databases
PRIDE	Q3UZD5.
Genome annotation databases
Ensembl	ENSMUST00000091900; ENSMUSP00000089513; ENSMUSG00000069378; Mus musculus. [Genome view]
GeneID	225518.
KEGG	mmu:225518.
UCSC	uc008exv.1. mouse.
Organism-specific databases
CTD	225518.
MGI	MGI:2684938. Prdm6.
Phylogenomic databases
eggNOG	roNOG08926.
HOGENOM	HBG506721.
HOVERGEN	Q3UZD5.
InParanoid	Q3UZD5.
OMA	LQPFSKS.
OrthoDB	EOG9QC3R8.
Gene expression databases
ArrayExpress	Q3UZD5.
Bgee	Q3UZD5.
Genevestigator	Q3UZD5.
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...
Other Resources
NextBio	377696.
SOURCE	Search...

Entry information

Entry name

PRDM6_MOUSE

Accession

Primary (citable) accession number: Q3UZD5
Secondary accession number(s): B9EIB0 , Q2I2X0, Q2I2X1, Q3UX75

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 10, 2009
Last sequence update:	October 11, 2005
Last modified:	February 9, 2010
This is version 47 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)