Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Putative histone-lysine N-methyltransferase PRDM6

Gene

PRDM6

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

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

Enzyme and pathway databases

BioCyciZFISH:HS00755-MONOMER.

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

HGNCiHGNC:9350. PRDM6.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Organism-specific databases

DisGeNETi93166.
OpenTargetsiENSG00000061455.
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.

PTM databases

iPTMnetiQ9NQX0.
PhosphoSitePlusiQ9NQX0.

Expressioni

Gene expression databases

BgeeiENSG00000061455.
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

Protein-protein interaction databases

BioGridi125009. 12 interactors.
IntActiQ9NQX0. 1 interactor.
STRINGi9606.ENSP00000384725.

Structurei

3D structure databases

ProteinModelPortaliQ9NQX0.
SMRiQ9NQX0.
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
Contains 4 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.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

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 (3)i

Sequence statusi: Complete.

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

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

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

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.
SMRiQ9NQX0.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi125009. 12 interactors.
IntActiQ9NQX0. 1 interactor.
STRINGi9606.ENSP00000384725.

PTM databases

iPTMnetiQ9NQX0.
PhosphoSitePlusiQ9NQX0.

Polymorphism and mutation databases

BioMutaiPRDM6.
DMDMi223590133.

Proteomic databases

PaxDbiQ9NQX0.
PeptideAtlasiQ9NQX0.
PRIDEiQ9NQX0.

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.
GeneCardsiPRDM6.
HGNCiHGNC:9350. PRDM6.
HPAiHPA030322.
HPA030324.
MIMi616982. gene.
neXtProtiNX_Q9NQX0.
OpenTargetsiENSG00000061455.
PharmGKBiPA33718.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

BioCyciZFISH:HS00755-MONOMER.

Miscellaneous databases

GenomeRNAii93166.
PROiQ9NQX0.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000061455.
CleanExiHS_PRDM6.
ExpressionAtlasiQ9NQX0. baseline and differential.
GenevisibleiQ9NQX0. HS.

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...

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 30, 2016
This is version 136 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. 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. 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.