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Protein

PHD finger protein 19

Gene

PHF19

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 RIOX1 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

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

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

  • DNA-binding transcription factor activity Source: GO_Central
  • metal ion binding Source: UniProtKB-KW
  • methylated histone binding Source: UniProtKB
  • sequence-specific DNA binding Source: GO_Central

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Repressor
Biological processTranscription, Transcription regulation
LigandMetal-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

EuPathDBiHostDB:ENSG00000119403.13
HGNCiHGNC:24566 PHF19
MIMi609740 gene
neXtProtiNX_Q5T6S3

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

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 RIOX1; when associated with A-56. 2 Publications1
Mutagenesisi56Y → A: Abolishes histone H3K36me3-binding. Abolishes histone H3K36me3-binding and recruitment of the PRC2 complex and RIOX1; 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
ProteomicsDBi64610
64611 [Q5T6S3-2]
64612 [Q5T6S3-3]

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 Expressed in 192 organ(s), highest expression level in esophagus
CleanExiHS_PHF19
ExpressionAtlasiQ5T6S3 baseline and differential
GenevisibleiQ5T6S3 HS

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 RIOX1.3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi117578, 34 interactors
IntActiQ5T6S3, 31 interactors
MINTiQ5T6S3
STRINGi9606.ENSP00000363003

Chemistry databases

BindingDBiQ5T6S3

Structurei

Secondary structure

1580
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

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, 1 hit
InterProiView protein in InterPro
IPR025894 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
PfamiView protein in Pfam
PF14061 Mtf2_C, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00249 PHD, 2 hits
SM00333 TUDOR, 1 hit
SUPFAMiSSF57903 SSF57903, 2 hits
PROSITEiView protein in PROSITE
PS01359 ZF_PHD_1, 2 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 6 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 6 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A0A087X169A0A087X169_HUMAN
PHD finger protein 19
PHF19
599Annotation score:
B0QZ72B0QZ72_HUMAN
PHD finger protein 19
PHF19
165Annotation score:
F5H8K3F5H8K3_HUMAN
PHD finger protein 19
PHF19
371Annotation score:
B0QZ50B0QZ50_HUMAN
PHD finger protein 19
PHF19
173Annotation score:
B0QZ51B0QZ51_HUMAN
PHD finger protein 19
PHF19
60Annotation score:
X6RER8X6RER8_HUMAN
PHD finger protein 19
PHF19
106Annotation score:

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.
AL161911 Genomic DNA No translation available.
AL354792 Genomic DNA No translation available.
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

Similar proteinsi

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.
AL161911 Genomic DNA No translation available.
AL354792 Genomic DNA No translation available.
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, 31 interactors
MINTiQ5T6S3
STRINGi9606.ENSP00000363003

Chemistry databases

BindingDBiQ5T6S3

PTM databases

iPTMnetiQ5T6S3
PhosphoSitePlusiQ5T6S3

Polymorphism and mutation databases

DMDMi74745265

Proteomic databases

EPDiQ5T6S3
MaxQBiQ5T6S3
PaxDbiQ5T6S3
PeptideAtlasiQ5T6S3
PRIDEiQ5T6S3
ProteomicsDBi64610
64611 [Q5T6S3-2]
64612 [Q5T6S3-3]

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
EuPathDBiHostDB:ENSG00000119403.13
GeneCardsiPHF19
HGNCiHGNC:24566 PHF19
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
PROiPR:Q5T6S3
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000119403 Expressed in 192 organ(s), highest expression level in esophagus
CleanExiHS_PHF19
ExpressionAtlasiQ5T6S3 baseline and differential
GenevisibleiQ5T6S3 HS

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR025894 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
PfamiView protein in Pfam
PF14061 Mtf2_C, 1 hit
PF00628 PHD, 1 hit
SMARTiView protein in SMART
SM00249 PHD, 2 hits
SM00333 TUDOR, 1 hit
SUPFAMiSSF57903 SSF57903, 2 hits
PROSITEiView protein in PROSITE
PS01359 ZF_PHD_1, 2 hits
ProtoNetiSearch...

Entry informationi

Entry nameiPHF19_HUMAN
AccessioniPrimary (citable) accession number: Q5T6S3
Secondary accession number(s): Q32NF2
, Q5T6S4, Q6N038, Q8TBL6, Q9UFS9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: February 5, 2008
Last sequence update: December 21, 2004
Last modified: November 7, 2018
This is version 132 of the entry and version 1 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  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. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
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