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Protein

Putative histone-lysine N-methyltransferase PRDM6

Gene

Prdm6

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

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 PubMed:16537907, it does not act as a histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to PubMed:17662997, 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.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N(6)-methyl-L-lysine-[histone].

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri474 – 49623C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri502 – 52423C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri530 – 55223C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri558 – 58023C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • negative regulation of smooth muscle cell differentiation Source: MGI
  • negative regulation of transcription, DNA-templated Source: MGI
  • neurogenesis Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Methyltransferase, Repressor, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, S-adenosyl-L-methionine, Zinc

Names & Taxonomyi

Protein namesi
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 namesi
Name:Prdm6
Synonyms:Gm92, Prism
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 18

Organism-specific databases

MGIiMGI:2684938. Prdm6.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 596596Putative histone-lysine N-methyltransferase PRDM6PRO_0000363959Add
BLAST

Proteomic databases

PaxDbiQ3UZD5.
PRIDEiQ3UZD5.

PTM databases

PhosphoSiteiQ3UZD5.

Expressioni

Tissue specificityi

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.2 Publications

Gene expression databases

BgeeiQ3UZD5.
GenevisibleiQ3UZD5. MM.

Interactioni

Subunit structurei

Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.1 Publication

GO - Molecular functioni

  • protein homodimerization activity Source: MGI

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000089513.

Structurei

3D structure databases

ProteinModelPortaliQ3UZD5.
SMRiQ3UZD5. Positions 200-375, 451-578.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini247 – 366120SETPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi30 – 356Poly-Gly
Compositional biasi49 – 8638Pro-richAdd
BLAST
Compositional biasi98 – 10710Poly-Ala
Compositional biasi124 – 1307Poly-Ala
Compositional biasi152 – 1565Poly-Gly
Compositional biasi229 – 2335Poly-Ala

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri474 – 49623C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri502 – 52423C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri530 – 55223C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri558 – 58023C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
ENOG410XRVC. LUCA.
GeneTreeiENSGT00830000128284.
HOGENOMiHOG000090218.
HOVERGENiHBG108289.
InParanoidiQ3UZD5.
OMAiPPEIPEW.
OrthoDBiEOG776SPN.
PhylomeDBiQ3UZD5.
TreeFamiTF106403.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 2 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q3UZD5-1) [UniParc]FASTAAdd to basket

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.

« Hide

        10         20         30         40         50
MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GGGGGPLKAS GAALALGAPQ
60 70 80 90 100
PLQPPPPPPP PPPERAEPPP DGLRPRPASL SSTPAPSSTS ASSASSCAAA
110 120 130 140 150
AAAAALAGLS ALPVAQMPVF APLAAAAVAA EPLPPKDLCL GASAGPGPAK
160 170 180 190 200
CGGGGGSVGD GRGVPRFRCS AEELDYYLYG QQRMEIIPLN QHTSDPNNRC
210 220 230 240 250
DMCADNRNGE CPMHGPLHSL RRLVGTSSAA AAAPPPELPE WLRDLPREVC
260 270 280 290 300
LCTSTVPGLA YGICAAQRIQ QGTWIGPFQG VLLSPEKVQT GVVRNTQHLW
310 320 330 340 350
EIYDQDGTLQ HFIDGGEPSK SSWMRYIRCA RHCGEQNLTV VQYRSNIFYR
360 370 380 390 400
ACIDIPRGTE LLVWYNDSYT SFFGIPLQCI AQDENLNVPS TVMEAMCRQD
410 420 430 440 450
ALQPFNKSSK LSPSGQQRSV VFPQTPCSRN FSLLDKSGPM EAGFNQINVK
460 470 480 490 500
NQRVLASPTS TSQLHSEFSD WHLWKCGQCF KTFTQRILLQ MHVCTQNPDR
510 520 530 540 550
PYQCGHCSQS FSQPSELRNH VVTHSSDRPF KCGYCGRAFA GATTLNNHIR
560 570 580 590
THTGEKPFKC ERCERSFTQA TQLSRHQRMP NECKPITESP ESIEVD
Length:596
Mass (Da):64,503
Last modified:October 11, 2005 - v1
Checksum:i1DEDC155893CC809
GO
Isoform 2 (identifier: Q3UZD5-2) [UniParc]FASTAAdd to basket

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

Show »
Length:395
Mass (Da):44,563
Checksum:iE5783499DAC230D5
GO
Isoform 3 (identifier: Q3UZD5-3) [UniParc]FASTAAdd to basket

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

Show »
Length:204
Mass (Da):23,214
Checksum:i5C0F29D2DBBCC701
GO
Isoform 4 (identifier: Q3UZD5-4) [UniParc]FASTAAdd to basket

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

Show »
Length:565
Mass (Da):61,756
Checksum:i680CC5ADB3468C1D
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 392392Missing in isoform 3. 1 PublicationVSP_036372Add
BLAST
Alternative sequencei1 – 201201Missing in isoform 2. 1 PublicationVSP_036371Add
BLAST
Alternative sequencei28 – 5831Missing in isoform 4. CuratedVSP_036373Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS29253.1. [Q3UZD5-1]
RefSeqiNP_001028453.1. NM_001033281.3. [Q3UZD5-1]
UniGeneiMm.297645.

Genome annotation databases

EnsembliENSMUST00000091900; ENSMUSP00000089513; ENSMUSG00000069378. [Q3UZD5-1]
ENSMUST00000115398; ENSMUSP00000111056; ENSMUSG00000069378. [Q3UZD5-3]
ENSMUST00000115399; ENSMUSP00000111057; ENSMUSG00000069378. [Q3UZD5-2]
GeneIDi225518.
KEGGimmu:225518.
UCSCiuc008exv.1. mouse. [Q3UZD5-1]
uc008exw.1. mouse. [Q3UZD5-3]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS29253.1. [Q3UZD5-1]
RefSeqiNP_001028453.1. NM_001033281.3. [Q3UZD5-1]
UniGeneiMm.297645.

3D structure databases

ProteinModelPortaliQ3UZD5.
SMRiQ3UZD5. Positions 200-375, 451-578.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000089513.

PTM databases

PhosphoSiteiQ3UZD5.

Proteomic databases

PaxDbiQ3UZD5.
PRIDEiQ3UZD5.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000091900; ENSMUSP00000089513; ENSMUSG00000069378. [Q3UZD5-1]
ENSMUST00000115398; ENSMUSP00000111056; ENSMUSG00000069378. [Q3UZD5-3]
ENSMUST00000115399; ENSMUSP00000111057; ENSMUSG00000069378. [Q3UZD5-2]
GeneIDi225518.
KEGGimmu:225518.
UCSCiuc008exv.1. mouse. [Q3UZD5-1]
uc008exw.1. mouse. [Q3UZD5-3]

Organism-specific databases

CTDi93166.
MGIiMGI:2684938. Prdm6.

Phylogenomic databases

eggNOGiKOG1721. Eukaryota.
KOG2461. Eukaryota.
ENOG410XRVC. LUCA.
GeneTreeiENSGT00830000128284.
HOGENOMiHOG000090218.
HOVERGENiHBG108289.
InParanoidiQ3UZD5.
OMAiPPEIPEW.
OrthoDBiEOG776SPN.
PhylomeDBiQ3UZD5.
TreeFamiTF106403.

Miscellaneous databases

ChiTaRSiPrdm6. mouse.
PROiQ3UZD5.
SOURCEiSearch...

Gene expression databases

BgeeiQ3UZD5.
GenevisibleiQ3UZD5. MM.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view]
PfamiPF00856. SET. 1 hit.
[Graphical view]
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 4 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 2 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract]
    Cited for: FUNCTION, ALTERNATIVE SPLICING (ISOFORM 4), SUBCELLULAR LOCATION, TISSUE SPECIFICITY.

Entry informationi

Entry nameiPRDM6_MOUSE
AccessioniPrimary (citable) accession number: Q3UZD5
Secondary accession number(s): B9EIB0
, Q2I2X0, Q2I2X1, Q3UX75
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: October 11, 2005
Last modified: June 8, 2016
This is version 99 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.