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Protein

PHD finger protein 19

Gene

PHF19

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Polycomb group (PcG) that specifically binds histone H3 trimethylated at 'Lys-36' (H3K36me3) and recruits the PRC2 complex. Probably involved in the transition from an active state to a repressed state in embryonic stem cells: acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting H3K36me3 histone demethylases NO66 or KDM2B, leading to demethylation of H3K36 and recruitment of the PRC2 complex that mediates H3K27me3 methylation, followed by de novo silencing. Recruits the PRC2 complex to CpG islands and contributes to embryonic stem cell self-renewal. Also binds dimethylated at 'Lys-36' (H3K36me2). Isoform 1 and isoform 2 inhibit transcription from an HSV-tk promoter.4 Publications

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei47Histone H3K36me31
Binding sitei55Histone H3K36me31

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri96 – 151PHD-type 1Add BLAST56
Zinc fingeri195 – 249PHD-type 2Add BLAST55

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB
  • zinc ion binding Source: InterPro

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-HSA-212300. PRC2 methylates histones and DNA.

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 19
Alternative name(s):
Polycomb-like protein 3
Short name:
hPCL3
Gene namesi
Name:PHF19
Synonyms:PCL3
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:24566. PHF19.

Subcellular locationi

  • Nucleus 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi50W → A in muthPhf19; abolishes histone H3K36me3-binding and impaired activity of the PRC2 complex and subsequent H3K27me3 methylation. 2 Publications1
Mutagenesisi50W → C: Abolishes histone H3K36me3-binding and recruitment of the PRC2 complex and NO66; when associated with A-56. 2 Publications1
Mutagenesisi56Y → A: Abolishes histone H3K36me3-binding. Abolishes histone H3K36me3-binding and recruitment of the PRC2 complex and NO66; when associated with C-50. 2 Publications1

Organism-specific databases

DisGeNETi26147.
OpenTargetsiENSG00000119403.
PharmGKBiPA134911501.

Polymorphism and mutation databases

DMDMi74745265.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003185701 – 580PHD finger protein 19Add BLAST580

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei13PhosphoserineCombined sources1
Modified residuei187PhosphoserineCombined sources1
Modified residuei365PhosphoserineCombined sources1
Modified residuei366PhosphoserineCombined sources1
Isoform 2 (identifier: Q5T6S3-2)
Modified residuei166PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiQ5T6S3.
MaxQBiQ5T6S3.
PaxDbiQ5T6S3.
PeptideAtlasiQ5T6S3.
PRIDEiQ5T6S3.

PTM databases

iPTMnetiQ5T6S3.
PhosphoSitePlusiQ5T6S3.

Expressioni

Tissue specificityi

Isoform 1 is expressed in thymus, heart, lung and kidney. Isoform 2 is predominantly expressed in placenta, skeletal muscle and kidney, whereas isoform 1 is predominantly expressed in liver and peripheral blood leukocytes. Overexpressed in many types of cancers, including colon, skin, lung, rectal, cervical, uterus, liver cancers, in cell lines derived from different stages of melanoma and in glioma cell lines.1 Publication

Gene expression databases

BgeeiENSG00000119403.
CleanExiHS_PHF19.
ExpressionAtlasiQ5T6S3. baseline and differential.
GenevisibleiQ5T6S3. HS.

Organism-specific databases

HPAiHPA051458.

Interactioni

Subunit structurei

Associated component of the PRC2 complex. Interacts with EZH2 (via its Tudor domain). Isoform 1 interacts with SUZ12; isoform 2 does not interact with SUZ12. Interacts with NO66.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
KDM1AO603412EBI-2339674,EBI-710124
SUV39H1O434632EBI-2339674,EBI-349968
SUV39H2Q9H5I12EBI-2339674,EBI-723127

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi117578. 34 interactors.
IntActiQ5T6S3. 18 interactors.
MINTiMINT-8417713.
STRINGi9606.ENSP00000363003.

Chemistry databases

BindingDBiQ5T6S3.

Structurei

Secondary structure

1580
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi45 – 49Combined sources5
Beta strandi55 – 60Combined sources6
Beta strandi68 – 74Combined sources7
Beta strandi79 – 83Combined sources5
Helixi84 – 86Combined sources3
Beta strandi87 – 89Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2E5QNMR-A40-95[»]
4BD3NMR-A38-95[»]
ProteinModelPortaliQ5T6S3.
SMRiQ5T6S3.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ5T6S3.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini40 – 93TudorAdd BLAST54

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni74 – 80Histone H3K36me3 binding7

Domaini

The Tudor domain recognizes and binds H3K36me3 (PubMed:23273982, PubMed:23160351, PubMed:23104054 and PubMed:23228662). May also bind H3K27me3, with a lower affinity (PubMed:23160351).2 Publications

Sequence similaritiesi

Belongs to the Polycomblike family.Curated
Contains 2 PHD-type zinc fingers.Curated
Contains 1 Tudor domain.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri96 – 151PHD-type 1Add BLAST56
Zinc fingeri195 – 249PHD-type 2Add BLAST55

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG4323. Eukaryota.
ENOG410XQ6E. LUCA.
GeneTreeiENSGT00390000009222.
HOGENOMiHOG000010307.
HOVERGENiHBG004755.
InParanoidiQ5T6S3.
KOiK11486.
PhylomeDBiQ5T6S3.
TreeFamiTF106420.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiIPR025894. Mtf2_C_dom.
IPR002999. Tudor.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF14061. Mtf2_C. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
SM00333. TUDOR. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 2 hits.
PROSITEiPS01359. ZF_PHD_1. 2 hits.
[Graphical view]

Sequences (3)i

Sequence statusi: Complete.

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

Isoform 1 (identifier: Q5T6S3-1) [UniParc]FASTAAdd to basket
Also known as: PCL3L, hPCL3L

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
MENRALDPGT RDSYGATSHL PNKGALAKVK NNFKDLMSKL TEGQYVLCRW
60 70 80 90 100
TDGLYYLGKI KRVSSSKQSC LVTFEDNSKY WVLWKDIQHA GVPGEEPKCN
110 120 130 140 150
ICLGKTSGPL NEILICGKCG LGYHQQCHIP IAGSADQPLL TPWFCRRCIF
160 170 180 190 200
ALAVRKGGAL KKGAIARTLQ AVKMVLSYQP EELEWDSPHR TNQQQCYCYC
210 220 230 240 250
GGPGEWYLRM LQCYRCRQWF HEACTQCLNE PMMFGDRFYL FFCSVCNQGP
260 270 280 290 300
EYIERLPLRW VDVVHLALYN LGVQSKKKYF DFEEILAFVN HHWELLQLGK
310 320 330 340 350
LTSTPVTDRG PHLLNALNSY KSRFLCGKEI KKKKCIFRLR IRVPPNPPGK
360 370 380 390 400
LLPDKGLLPN ENSASSELRK RGKSKPGLLP HEFQQQKRRV YRRKRSKFLL
410 420 430 440 450
EDAIPSSDFT SAWSTNHHLA SIFDFTLDEI QSLKSASSGQ TFFSDVDSTD
460 470 480 490 500
AASTSGSAST SLSYDSRWTV GSRKRKLAAK AYMPLRAKRW AAELDGRCPS
510 520 530 540 550
DSSAEGASVP ERPDEGIDSH TFESISEDDS SLSHLKSSIT NYFGAAGRLA
560 570 580
CGEKYQVLAR RVTPEGKVQY LVEWEGTTPY
Length:580
Mass (Da):65,591
Last modified:December 21, 2004 - v1
Checksum:i17CCF21BA2827826
GO
Isoform 2 (identifier: Q5T6S3-2) [UniParc]FASTAAdd to basket
Also known as: PCL3S, hPCL3S

The sequence of this isoform differs from the canonical sequence as follows:
     155-207: RKGGALKKGA...CYCGGPGEWY → RVSLPSSPVP...ASATVLGQDL
     208-580: Missing.

Show »
Length:207
Mass (Da):22,512
Checksum:i34F3EF834B17FAF0
GO
Isoform 3 (identifier: Q5T6S3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     122-130: GYHQQCHIP → VPHPHSGQC
     131-580: Missing.

Show »
Length:130
Mass (Da):14,386
Checksum:iE10645A3F782774C
GO

Sequence cautioni

The sequence CAE45832 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti181E → G in CAE45832 (PubMed:17974005).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_031222122 – 130GYHQQCHIP → VPHPHSGQC in isoform 3. 1 Publication9
Alternative sequenceiVSP_031223131 – 580Missing in isoform 3. 1 PublicationAdd BLAST450
Alternative sequenceiVSP_031224155 – 207RKGGA…PGEWY → RVSLPSSPVPASPASSSGAD QRLPSQSLSSKQKGHTWALE TDSASATVLGQDL in isoform 2. 1 PublicationAdd BLAST53
Alternative sequenceiVSP_031225208 – 580Missing in isoform 2. 1 PublicationAdd BLAST373

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL117477 mRNA. Translation: CAB55950.1.
BX640713 mRNA. Translation: CAE45832.1. Different initiation.
AL354792 Genomic DNA. Translation: CAI15690.1.
AL354792 Genomic DNA. Translation: CAI15691.1.
AL354792, AL161911 Genomic DNA. Translation: CAI15692.1.
AL161911, AL354792 Genomic DNA. Translation: CAI95112.1.
BC022374 mRNA. Translation: AAH22374.1.
BC108663 mRNA. Translation: AAI08664.1.
BC125076 mRNA. Translation: AAI25077.1.
BC125077 mRNA. Translation: AAI25078.1.
CCDSiCCDS35116.1. [Q5T6S3-1]
CCDS35117.1. [Q5T6S3-2]
PIRiT17260.
RefSeqiNP_001009936.1. NM_001009936.2. [Q5T6S3-2]
NP_001273769.1. NM_001286840.1.
NP_001273772.1. NM_001286843.1. [Q5T6S3-3]
NP_056466.1. NM_015651.2. [Q5T6S3-1]
XP_005251963.1. XM_005251906.2. [Q5T6S3-1]
XP_011516811.1. XM_011518509.2. [Q5T6S3-1]
XP_016870101.1. XM_017014612.1. [Q5T6S3-1]
UniGeneiHs.460124.

Genome annotation databases

EnsembliENST00000312189; ENSP00000310372; ENSG00000119403. [Q5T6S3-2]
ENST00000373896; ENSP00000363003; ENSG00000119403. [Q5T6S3-1]
GeneIDi26147.
KEGGihsa:26147.
UCSCiuc004bks.3. human. [Q5T6S3-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AL117477 mRNA. Translation: CAB55950.1.
BX640713 mRNA. Translation: CAE45832.1. Different initiation.
AL354792 Genomic DNA. Translation: CAI15690.1.
AL354792 Genomic DNA. Translation: CAI15691.1.
AL354792, AL161911 Genomic DNA. Translation: CAI15692.1.
AL161911, AL354792 Genomic DNA. Translation: CAI95112.1.
BC022374 mRNA. Translation: AAH22374.1.
BC108663 mRNA. Translation: AAI08664.1.
BC125076 mRNA. Translation: AAI25077.1.
BC125077 mRNA. Translation: AAI25078.1.
CCDSiCCDS35116.1. [Q5T6S3-1]
CCDS35117.1. [Q5T6S3-2]
PIRiT17260.
RefSeqiNP_001009936.1. NM_001009936.2. [Q5T6S3-2]
NP_001273769.1. NM_001286840.1.
NP_001273772.1. NM_001286843.1. [Q5T6S3-3]
NP_056466.1. NM_015651.2. [Q5T6S3-1]
XP_005251963.1. XM_005251906.2. [Q5T6S3-1]
XP_011516811.1. XM_011518509.2. [Q5T6S3-1]
XP_016870101.1. XM_017014612.1. [Q5T6S3-1]
UniGeneiHs.460124.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2E5QNMR-A40-95[»]
4BD3NMR-A38-95[»]
ProteinModelPortaliQ5T6S3.
SMRiQ5T6S3.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi117578. 34 interactors.
IntActiQ5T6S3. 18 interactors.
MINTiMINT-8417713.
STRINGi9606.ENSP00000363003.

Chemistry databases

BindingDBiQ5T6S3.

PTM databases

iPTMnetiQ5T6S3.
PhosphoSitePlusiQ5T6S3.

Polymorphism and mutation databases

DMDMi74745265.

Proteomic databases

EPDiQ5T6S3.
MaxQBiQ5T6S3.
PaxDbiQ5T6S3.
PeptideAtlasiQ5T6S3.
PRIDEiQ5T6S3.

Protocols and materials databases

DNASUi26147.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000312189; ENSP00000310372; ENSG00000119403. [Q5T6S3-2]
ENST00000373896; ENSP00000363003; ENSG00000119403. [Q5T6S3-1]
GeneIDi26147.
KEGGihsa:26147.
UCSCiuc004bks.3. human. [Q5T6S3-1]

Organism-specific databases

CTDi26147.
DisGeNETi26147.
GeneCardsiPHF19.
HGNCiHGNC:24566. PHF19.
HPAiHPA051458.
MIMi609740. gene.
neXtProtiNX_Q5T6S3.
OpenTargetsiENSG00000119403.
PharmGKBiPA134911501.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4323. Eukaryota.
ENOG410XQ6E. LUCA.
GeneTreeiENSGT00390000009222.
HOGENOMiHOG000010307.
HOVERGENiHBG004755.
InParanoidiQ5T6S3.
KOiK11486.
PhylomeDBiQ5T6S3.
TreeFamiTF106420.

Enzyme and pathway databases

ReactomeiR-HSA-212300. PRC2 methylates histones and DNA.

Miscellaneous databases

ChiTaRSiPHF19. human.
EvolutionaryTraceiQ5T6S3.
GenomeRNAii26147.
PROiQ5T6S3.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000119403.
CleanExiHS_PHF19.
ExpressionAtlasiQ5T6S3. baseline and differential.
GenevisibleiQ5T6S3. HS.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiIPR025894. Mtf2_C_dom.
IPR002999. Tudor.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF14061. Mtf2_C. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 2 hits.
SM00333. TUDOR. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 2 hits.
PROSITEiPS01359. ZF_PHD_1. 2 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHF19_HUMAN
AccessioniPrimary (citable) accession number: Q5T6S3
Secondary accession number(s): Q32NF2
, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: December 21, 2004
Last modified: November 30, 2016
This is version 119 of the entry and version 1 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

Miscellaneous

Down-regulated in spheroid melanoma cells that display an invasive phenotype, characterized by a higher motility, a poor proliferation rate and a gain of pluripotency gene expression. PHF19 favors the proliferation and reduces the transmigration capacity of melanoma cell lines, 2 properties of invasive cells, suggesting that down-regulation may participate in the switch from proliferative to invasive states in melanoma cells (PubMed:22487681).1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.