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Protein

Putative histone-lysine N-methyltransferase PRDM6

Gene

PRDM6

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 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 activityi

S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine + N6-methyl-L-lysine-[histone].

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri473 – 495C2H2-type 1; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri501 – 523C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri529 – 551C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri557 – 579C2H2-type 4; degeneratePROSITE-ProRule annotationAdd BLAST23

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Methyltransferase, Repressor, Transferase
Biological processTranscription, Transcription regulation
LigandMetal-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
Proteomesi
  • UP000005640 Componenti: Chromosome 5

Organism-specific databases

EuPathDBiHostDB:ENSG00000061455.10
HGNCiHGNC:9350 PRDM6
MIMi616982 gene
neXtProtiNX_Q9NQX0

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Patent ductus arteriosus 3 (PDA3)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA congenital heart defect characterized by the persistent opening of fetal ductus arteriosus that fails to close after birth. Fetal ductus arteriosus connects the pulmonary artery to the descending aorta, allowing unoxygenated blood to bypass the lung and flow to the placenta. Normally, the ductus occludes shortly after birth.
See also OMIM:617039
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_077014263C → S in PDA3; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs879255279EnsemblClinVar.1
Natural variantiVAR_077015462Q → R in PDA3. 1 PublicationCorresponds to variant dbSNP:rs879253872EnsemblClinVar.1
Natural variantiVAR_077016549R → Q in PDA3. 1 PublicationCorresponds to variant dbSNP:rs879255278EnsemblClinVar.1

Keywords - Diseasei

Disease mutation

Organism-specific databases

DisGeNETi93166
MalaCardsiPRDM6
MIMi617039 phenotype
OpenTargetsiENSG00000061455
Orphaneti466729 Familial patent arterial duct
PharmGKBiPA33718

Polymorphism and mutation databases

BioMutaiPRDM6
DMDMi223590133

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477621 – 595Putative histone-lysine N-methyltransferase PRDM6Add BLAST595

Proteomic databases

PaxDbiQ9NQX0
PeptideAtlasiQ9NQX0
PRIDEiQ9NQX0
ProteomicsDBi82215
82216 [Q9NQX0-1]
82217 [Q9NQX0-2]

PTM databases

iPTMnetiQ9NQX0
PhosphoSitePlusiQ9NQX0

Expressioni

Gene expression databases

BgeeiENSG00000061455 Expressed in 126 organ(s), highest expression level in descending thoracic aorta
CleanExiHS_PRDM6
ExpressionAtlasiQ9NQX0 baseline and differential
GenevisibleiQ9NQX0 HS

Organism-specific databases

HPAiHPA030322
HPA030324

Interactioni

Subunit structurei

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

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi125009, 12 interactors
IntActiQ9NQX0, 70 interactors
MINTiQ9NQX0
STRINGi9606.ENSP00000384725

Structurei

3D structure databases

ProteinModelPortaliQ9NQX0
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini246 – 365SETPROSITE-ProRule annotationAdd BLAST120

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi47 – 73Pro-richAdd BLAST27
Compositional biasi97 – 106Poly-Ala10
Compositional biasi123 – 129Poly-Ala7
Compositional biasi151 – 162Poly-GlyAdd BLAST12
Compositional biasi228 – 232Poly-Ala5

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri473 – 495C2H2-type 1; degeneratePROSITE-ProRule annotationAdd BLAST23
Zinc fingeri501 – 523C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri529 – 551C2H2-type 3PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri557 – 579C2H2-type 4; degeneratePROSITE-ProRule annotationAdd BLAST23

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG1721 Eukaryota
KOG2461 Eukaryota
ENOG410XRVC LUCA
GeneTreeiENSGT00830000128284
HOGENOMiHOG000090218
HOVERGENiHBG108289
InParanoidiQ9NQX0
KOiK20795
OMAiPPEIPEW
OrthoDBiEOG091G0A5R
PhylomeDBiQ9NQX0
TreeFamiTF106403

Family and domain databases

InterProiView protein in InterPro
IPR001214 SET_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF00096 zf-C2H2, 3 hits
SMARTiView protein in SMART
SM00317 SET, 1 hit
SM00355 ZnF_C2H2, 4 hits
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 2 hits
PS50157 ZINC_FINGER_C2H2_2, 4 hits

Sequences (3+)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 3 described isoforms and 1 potential isoform that is computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There is 1 potential isoform mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H7BZR2H7BZR2_HUMAN
Putative histone-lysine N-methyltra...
PRDM6
73Annotation score:

Sequence cautioni

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_077014263C → S in PDA3; unknown pathological significance. 1 PublicationCorresponds to variant dbSNP:rs879255279EnsemblClinVar.1
Natural variantiVAR_077015462Q → R in PDA3. 1 PublicationCorresponds to variant dbSNP:rs879253872EnsemblClinVar.1
Natural variantiVAR_077016549R → Q in PDA3. 1 PublicationCorresponds to variant dbSNP:rs879255278EnsemblClinVar.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0363481 – 182Missing in isoform 2 and isoform 3. 1 PublicationAdd BLAST182
Alternative sequenceiVSP_006929314 – 595Missing in isoform 2. 1 PublicationAdd BLAST282

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]
UniGeneiHs.135118

Genome annotation databases

EnsembliENST00000407847; ENSP00000384725; ENSG00000061455 [Q9NQX0-3]
GeneIDi93166
KEGGihsa:93166
UCSCiuc003kti.4 human [Q9NQX0-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

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.
CCDSiCCDS47259.1 [Q9NQX0-3]
RefSeqiNP_001129711.1, NM_001136239.1 [Q9NQX0-3]
UniGeneiHs.135118

3D structure databases

ProteinModelPortaliQ9NQX0
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125009, 12 interactors
IntActiQ9NQX0, 70 interactors
MINTiQ9NQX0
STRINGi9606.ENSP00000384725

PTM databases

iPTMnetiQ9NQX0
PhosphoSitePlusiQ9NQX0

Polymorphism and mutation databases

BioMutaiPRDM6
DMDMi223590133

Proteomic databases

PaxDbiQ9NQX0
PeptideAtlasiQ9NQX0
PRIDEiQ9NQX0
ProteomicsDBi82215
82216 [Q9NQX0-1]
82217 [Q9NQX0-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000407847; ENSP00000384725; ENSG00000061455 [Q9NQX0-3]
GeneIDi93166
KEGGihsa:93166
UCSCiuc003kti.4 human [Q9NQX0-3]

Organism-specific databases

CTDi93166
DisGeNETi93166
EuPathDBiHostDB:ENSG00000061455.10
GeneCardsiPRDM6
HGNCiHGNC:9350 PRDM6
HPAiHPA030322
HPA030324
MalaCardsiPRDM6
MIMi616982 gene
617039 phenotype
neXtProtiNX_Q9NQX0
OpenTargetsiENSG00000061455
Orphaneti466729 Familial patent arterial duct
PharmGKBiPA33718
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG1721 Eukaryota
KOG2461 Eukaryota
ENOG410XRVC LUCA
GeneTreeiENSGT00830000128284
HOGENOMiHOG000090218
HOVERGENiHBG108289
InParanoidiQ9NQX0
KOiK20795
OMAiPPEIPEW
OrthoDBiEOG091G0A5R
PhylomeDBiQ9NQX0
TreeFamiTF106403

Miscellaneous databases

GenomeRNAii93166
PROiPR:Q9NQX0
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000061455 Expressed in 126 organ(s), highest expression level in descending thoracic aorta
CleanExiHS_PRDM6
ExpressionAtlasiQ9NQX0 baseline and differential
GenevisibleiQ9NQX0 HS

Family and domain databases

InterProiView protein in InterPro
IPR001214 SET_dom
IPR036236 Znf_C2H2_sf
IPR013087 Znf_C2H2_type
PfamiView protein in Pfam
PF00856 SET, 1 hit
PF00096 zf-C2H2, 3 hits
SMARTiView protein in SMART
SM00317 SET, 1 hit
SM00355 ZnF_C2H2, 4 hits
SUPFAMiSSF57667 SSF57667, 2 hits
PROSITEiView protein in PROSITE
PS50280 SET, 1 hit
PS00028 ZINC_FINGER_C2H2_1, 2 hits
PS50157 ZINC_FINGER_C2H2_2, 4 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPRDM6_HUMAN
AccessioniPrimary (citable) accession number: Q9NQX0
Secondary accession number(s): B5MCJ4, Q9NQW9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: February 10, 2009
Last modified: November 7, 2018
This is version 153 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. Human chromosome 5
    Human chromosome 5: entries, gene names and cross-references to MIM
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Main funding by: National Institutes of Health

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