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Q9NQX0

- PRDM6_HUMAN

UniProt

Q9NQX0 - PRDM6_HUMAN

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Protein

Putative histone-lysine N-methyltransferase PRDM6

Gene

PRDM6

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript 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 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).By similarity

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 fingeri473 – 49523C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri501 – 52323C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri529 – 55123C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri557 – 57923C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. histone-lysine N-methyltransferase activity Source: UniProtKB-EC
  2. metal ion binding Source: UniProtKB-KW
  3. nucleic acid binding Source: InterPro

GO - Biological processi

  1. negative regulation of smooth muscle cell differentiation Source: Ensembl
  2. negative regulation of transcription, DNA-templated Source: Ensembl
  3. neurogenesis Source: Ensembl
  4. 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
Gene namesi
Name:PRDM6
Synonyms:PFM3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 5

Organism-specific databases

HGNCiHGNC:9350. PRDM6.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA33718.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 595595Putative histone-lysine N-methyltransferase PRDM6PRO_0000047762Add
BLAST

Proteomic databases

PaxDbiQ9NQX0.
PRIDEiQ9NQX0.

PTM databases

PhosphoSiteiQ9NQX0.

Expressioni

Gene expression databases

BgeeiQ9NQX0.
CleanExiHS_PRDM6.
GenevestigatoriQ9NQX0.

Organism-specific databases

HPAiHPA030322.
HPA030324.

Interactioni

Subunit structurei

Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300.By similarity

Protein-protein interaction databases

BioGridi125009. 9 interactions.

Structurei

3D structure databases

ProteinModelPortaliQ9NQX0.
SMRiQ9NQX0. Positions 199-374, 450-577.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini246 – 365120SETPROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi47 – 7327Pro-richAdd
BLAST
Compositional biasi97 – 10610Poly-Ala
Compositional biasi123 – 1297Poly-Ala
Compositional biasi151 – 16212Poly-GlyAdd
BLAST
Compositional biasi228 – 2325Poly-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 fingeri473 – 49523C2H2-type 1; degeneratePROSITE-ProRule annotationAdd
BLAST
Zinc fingeri501 – 52323C2H2-type 2PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri529 – 55123C2H2-type 3PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri557 – 57923C2H2-type 4; degeneratePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG325470.
GeneTreeiENSGT00770000120502.
HOGENOMiHOG000090218.
HOVERGENiHBG108289.
InParanoidiQ9NQX0.
OMAiIVFPQTP.
OrthoDBiEOG776SPN.
PhylomeDBiQ9NQX0.
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.
PF00096. zf-C2H2. 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 (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. Align

Isoform 1 (identifier: Q9NQX0-3) [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 GAGPLKGSGA AGLLSAPQPL
60 70 80 90 100
QPPPPPPPPE RAEPPPDSLR PRPASLSSAS STPASSSTSA SSASSCAAAA
110 120 130 140 150
AAAALAGLSA LPVSQLPVFA PLAAAAVAAE PLPPKELCLG ATSGPGPVKC
160 170 180 190 200
GGGGGGGGEG RGAPRFRCSA EELDYYLYGQ QRMEIIPLNQ HTSDPNNRCD
210 220 230 240 250
MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW LRDLPREVCL
260 270 280 290 300
CTSTVPGLAY GICAAQRIQQ GTWIGPFQGV LLPPEKVQAG AVRNTQHLWE
310 320 330 340 350
IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA
360 370 380 390 400
CIDIPRGTEL LVWYNDSYTS FFGIPLQCIA QDENLNVPST VMEAMCRQDA
410 420 430 440 450
LQPFNKSSKL APTTQQRSVV FPQTPCSRNF SLLDKSGPIE SGFNQINVKN
460 470 480 490 500
QRVLASPTST SQLHSEFSDW HLWKCGQCFK TFTQRILLQM HVCTQNPDRP
510 520 530 540 550
YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG ATTLNNHIRT
560 570 580 590
HTGEKPFKCE RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD
Length:595
Mass (Da):64,452
Last modified:February 10, 2009 - v2
Checksum:iDB8D815E7C107451
GO
Isoform 2 (identifier: Q9NQX0-2) [UniParc]FASTAAdd to Basket

Also known as: B

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

Show »
Length:131
Mass (Da):14,436
Checksum:i1C608683110D5DC2
GO
Isoform 3 (identifier: Q9NQX0-1) [UniParc]FASTAAdd to Basket

Also known as: A

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

Show »
Length:413
Mass (Da):46,635
Checksum:i9D5FCB5B9F885666
GO

Sequence cautioni

The sequence AAF78078.1 differs from that shown. Reason: Erroneous initiation. Curated
The sequence AAF78079.1 differs from that shown. Reason: Erroneous initiation. Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 182182Missing in isoform 2 and isoform 3. 1 PublicationVSP_036348Add
BLAST
Alternative sequencei314 – 595282Missing in isoform 2. 1 PublicationVSP_006929Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSiCCDS47259.1. [Q9NQX0-3]
RefSeqiNP_001129711.1. NM_001136239.1. [Q9NQX0-3]
XP_005272185.1. XM_005272128.2. [Q9NQX0-3]
UniGeneiHs.135118.

Genome annotation databases

EnsembliENST00000407847; ENSP00000384725; ENSG00000061455. [Q9NQX0-3]
GeneIDi93166.
KEGGihsa:93166.
UCSCiuc003kti.3. human. [Q9NQX0-3]

Polymorphism databases

DMDMi223590133.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
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.
CCDSi CCDS47259.1. [Q9NQX0-3 ]
RefSeqi NP_001129711.1. NM_001136239.1. [Q9NQX0-3 ]
XP_005272185.1. XM_005272128.2. [Q9NQX0-3 ]
UniGenei Hs.135118.

3D structure databases

ProteinModelPortali Q9NQX0.
SMRi Q9NQX0. Positions 199-374, 450-577.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 125009. 9 interactions.

PTM databases

PhosphoSitei Q9NQX0.

Polymorphism databases

DMDMi 223590133.

Proteomic databases

PaxDbi Q9NQX0.
PRIDEi Q9NQX0.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000407847 ; ENSP00000384725 ; ENSG00000061455 . [Q9NQX0-3 ]
GeneIDi 93166.
KEGGi hsa:93166.
UCSCi uc003kti.3. human. [Q9NQX0-3 ]

Organism-specific databases

CTDi 93166.
GeneCardsi GC05P122424.
HGNCi HGNC:9350. PRDM6.
HPAi HPA030322.
HPA030324.
neXtProti NX_Q9NQX0.
PharmGKBi PA33718.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG325470.
GeneTreei ENSGT00770000120502.
HOGENOMi HOG000090218.
HOVERGENi HBG108289.
InParanoidi Q9NQX0.
OMAi IVFPQTP.
OrthoDBi EOG776SPN.
PhylomeDBi Q9NQX0.
TreeFami TF106403.

Miscellaneous databases

GenomeRNAii 93166.
NextBioi 78013.
PROi Q9NQX0.

Gene expression databases

Bgeei Q9NQX0.
CleanExi HS_PRDM6.
Genevestigatori Q9NQX0.

Family and domain databases

Gene3Di 3.30.160.60. 3 hits.
InterProi IPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
[Graphical view ]
Pfami PF00856. SET. 1 hit.
PF00096. zf-C2H2. 1 hit.
[Graphical view ]
SMARTi SM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 4 hits.
[Graphical view ]
PROSITEi PS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 2 hits.
PS50157. ZINC_FINGER_C2H2_2. 4 hits.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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].

Entry informationi

Entry nameiPRDM6_HUMAN
AccessioniPrimary (citable) accession number: Q9NQX0
Secondary accession number(s): B5MCJ4, Q9NQW9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: February 10, 2009
Last modified: November 26, 2014
This is version 118 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny 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.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3