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Protein

PHD finger protein 1

Gene

PHF1

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. Involved in DNA damage response and is recruited at double-strand breaks (DSBs). Acts by binding to H3K36me3, a mark for transcriptional activation, and recruiting the PRC2 complex: it is however unclear whether recruitment of the PRC2 complex to H3K36me3 leads to enhance or inhibit H3K27me3 methylation mediated by the PRC2 complex. According to some reports, PRC2 recruitment by PHF1 promotes H3K27me3 and subsequent gene silencing by inducing spreading of PRC2 and H3K27me3 into H3K36me3 loci (PubMed:18285464 and PubMed:23273982). According to another report, PHF1 recruits the PRC2 complex at double-strand breaks (DSBs) and inhibits the activity of PRC2 (PubMed:23142980). Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53.6 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri87 – 142PHD-type 1PROSITE-ProRule annotationAdd BLAST56
Zinc fingeri186 – 240PHD-type 2PROSITE-ProRule annotationAdd BLAST55

GO - Molecular functioni

  • chromatin binding Source: Ensembl
  • 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 processDNA damage, Transcription, 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 1
Short name:
Protein PHF1
Short name:
hPHF1
Alternative name(s):
Polycomb-like protein 1
Short name:
hPCl1
Gene namesi
Name:PHF1
Synonyms:PCL1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

EuPathDBiHostDB:ENSG00000112511.17
HGNCiHGNC:8919 PHF1
MIMi602881 gene
neXtProtiNX_O43189

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

Cytoplasm, Cytoskeleton, Nucleus

Pathology & Biotechi

Involvement in diseasei

A chromosomal aberration involving PHF1 may be a cause of endometrial stromal tumors. Translocation t(6;7)(p21;p22) with JAZF1. Translocation t(1;6)(p34;p21) with MEAF6.2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi41W → A: Abolishes histone H3K36me3-binding and localization at double-strand breaks (DSBs). 2 Publications1
Mutagenesisi47Y → A: Abolishes histone H3K36me3-binding. 2 Publications1
Mutagenesisi65F → A: Abolishes histone H3K36me3-binding. 1 Publication1
Mutagenesisi66E → K: Impairs histone H3K36me3-binding. 1 Publication1
Mutagenesisi71F → A: Abolishes histone H3K36me3-binding. 1 Publication1

Organism-specific databases

DisGeNETi5252
OpenTargetsiENSG00000112511
PharmGKBiPA33259

Polymorphism and mutation databases

BioMutaiPHF1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000592881 – 567PHD finger protein 1Add BLAST567

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei420PhosphoserineCombined sources1
Isoform 1 (identifier: O43189-2)
Modified residuei360PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiO43189
MaxQBiO43189
PaxDbiO43189
PeptideAtlasiO43189
PRIDEiO43189
ProteomicsDBi48805
48806 [O43189-2]

PTM databases

iPTMnetiO43189
PhosphoSitePlusiO43189

Expressioni

Tissue specificityi

Highest levels in heart, skeletal muscle, and pancreas, lower levels in brain, placenta, lung, liver and kidney.

Gene expression databases

BgeeiENSG00000112511 Expressed in 232 organ(s), highest expression level in left testis
CleanExiHS_PHF1
ExpressionAtlasiO43189 baseline and differential
GenevisibleiO43189 HS

Organism-specific databases

HPAiHPA031038

Interactioni

Subunit structurei

Interacts with CHMP1 (By similarity). Associated component of the PRC2 complex. Interacts with p53/TP53.By similarity3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi111271, 57 interactors
DIPiDIP-34001N
IntActiO43189, 80 interactors
MINTiO43189
STRINGi9606.ENSP00000363640

Chemistry databases

BindingDBiO43189

Structurei

Secondary structure

1567
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliO43189
SMRiO43189
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO43189

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini29 – 86TudorAdd BLAST58

Domaini

The Tudor domain recognizes and binds H3K36me3 (PubMed:23228662, PubMed:23273982 and PubMed:23142980).

Sequence similaritiesi

Belongs to the Polycomblike family.Curated

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri87 – 142PHD-type 1PROSITE-ProRule annotationAdd BLAST56
Zinc fingeri186 – 240PHD-type 2PROSITE-ProRule annotationAdd BLAST55

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiKOG4323 Eukaryota
ENOG410XQ6E LUCA
GeneTreeiENSGT00390000009222
HOVERGENiHBG004755
InParanoidiO43189
KOiK11467
OMAiAPPLWDP
OrthoDBiEOG091G01JL
PhylomeDBiO43189
TreeFamiTF106420

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR025894 Mtf2_C_dom
IPR031202 PHF1
IPR002999 Tudor
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PANTHERiPTHR12628:SF11 PTHR12628:SF11, 1 hit
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
PS50016 ZF_PHD_2, 1 hit

Sequences (2+)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 2 described isoforms and 10 potential isoforms that are computationally mapped.Show allAlign All

Isoform 2 (identifier: O43189-1) [UniParc]FASTAAdd to basket
Also known as: PHF2

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
MAQPPRLSRS GASSLWDPAS PAPTSGPRPR LWEGQDVLAR WTDGLLYLGT
60 70 80 90 100
IKKVDSAREV CLVQFEDDSQ FLVLWKDISP AALPGEELLC CVCRSETVVP
110 120 130 140 150
GNRLVSCEKC RHAYHQDCHV PRAPAPGEGE GTSWVCRQCV FAIATKRGGA
160 170 180 190 200
LKKGPYARAM LGMKLSLPYG LKGLDWDAGH LSNRQQSYCY CGGPGEWNLK
210 220 230 240 250
MLQCRSCLQW FHEACTQCLS KPLLYGDRFY EFECCVCRGG PEKVRRLQLR
260 270 280 290 300
WVDVAHLVLY HLSVCCKKKY FDFDREILPF TSENWDSLLL GELSDTPKGE
310 320 330 340 350
RSSRLLSALN SHKDRFISGR EIKKRKCLFG LHARMPPPVE PPTGDGALTS
360 370 380 390 400
FPSGQGPGGG VSRPLGKRRR PEPEPLRRRQ KGKVEELGPP SAVRNQPEPQ
410 420 430 440 450
EQRERAHLQR ALQASVSPPS PSPNQSYQGS SGYNFRPTDA RCLPSSPIRM
460 470 480 490 500
FASFHPSAST AGTSGDSGPP DRSPLELHIG FPTDIPKSAP HSMTASSSSV
510 520 530 540 550
SSPSPGLPRR SAPPSPLCRS LSPGTGGGVR GGVGYLSRGD PVRVLARRVR
560
PDGSVQYLVE WGGGGIF
Length:567
Mass (Da):62,106
Last modified:January 11, 2011 - v3
Checksum:iE81BA9475565957C
GO
Isoform 1 (identifier: O43189-2) [UniParc]FASTAAdd to basket
Also known as: PHF1

The sequence of this isoform differs from the canonical sequence as follows:
     350-457: SFPSGQGPGG...IRMFASFHPS → RAGPWGRGLT...QTSLKVPPTR
     458-567: Missing.

Show »
Length:457
Mass (Da):49,643
Checksum:i611EF2B5A416841C
GO

Computationally mapped potential isoform sequencesi

There are 10 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
A2AB23A2AB23_HUMAN
PHD finger protein 1
PHF1
227Annotation score:
E9PQZ5E9PQZ5_HUMAN
PHD finger protein 1
PHF1
393Annotation score:
A2AB22A2AB22_HUMAN
PHD finger protein 1
PHF1
145Annotation score:
E9PQT8E9PQT8_HUMAN
PHD finger protein 1
PHF1
419Annotation score:
A0A140TA01A0A140TA01_HUMAN
PHD finger protein 1
PHF1
393Annotation score:
A0A087WVG4A0A087WVG4_HUMAN
PHD finger protein 1
PHF1
54Annotation score:
A0A0G2JIJ9A0A0G2JIJ9_HUMAN
PHD finger protein 1
PHF1
181Annotation score:
A0A140T9U3A0A140T9U3_HUMAN
PHD finger protein 1
PHF1
243Annotation score:
A2AB25A2AB25_HUMAN
PHD finger protein 1
PHF1
37Annotation score:
A0A140TA07A0A140TA07_HUMAN
PHD finger protein 1
PHF1
54Annotation score:

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04450042T → S. Corresponds to variant dbSNP:rs6934613Ensembl.1
Natural variantiVAR_034382304R → K5 PublicationsCorresponds to variant dbSNP:rs3116713Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_004694350 – 457SFPSG…SFHPS → RAGPWGRGLTSPGEAPEAGA RAPEEEAEGESGGAGATLSS AQSARAPGAEGAGSSAEGTA AAPSGCLLPSTLLPAPQGPL GTVDPQTGHPWNFTLVSPQT SLKVPPTR in isoform 1. 1 PublicationAdd BLAST108
Alternative sequenceiVSP_004695458 – 567Missing in isoform 1. 1 PublicationAdd BLAST110

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF029678 mRNA Translation: AAC52062.1
AF052205 mRNA Translation: AAC13273.1
AL662799 Genomic DNA No translation available.
AL021366 Genomic DNA Translation: CAA16158.1
AL021366 Genomic DNA Translation: CAA16159.1
AL050332 Genomic DNA Translation: CAC38366.1
AL050332 Genomic DNA Translation: CAC38367.1
BX088650 Genomic DNA No translation available.
CH471081 Genomic DNA Translation: EAX03729.1
CH471081 Genomic DNA Translation: EAX03730.1
BC008834 mRNA Translation: AAH08834.1
CCDSiCCDS4777.1 [O43189-1]
CCDS4778.1 [O43189-2]
RefSeqiNP_002627.1, NM_002636.4
NP_077084.1, NM_024165.2
XP_011512964.1, XM_011514662.1 [O43189-1]
UniGeneiHs.166204

Genome annotation databases

EnsembliENST00000374512; ENSP00000363636; ENSG00000112511 [O43189-2]
ENST00000374516; ENSP00000363640; ENSG00000112511 [O43189-1]
ENST00000427869; ENSP00000391901; ENSG00000225553
ENST00000454914; ENSP00000407295; ENSG00000225553
GeneIDi5252
KEGGihsa:5252
UCSCiuc003oeh.4 human [O43189-1]

Keywords - Coding sequence diversityi

Alternative splicing, Chromosomal rearrangement, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF029678 mRNA Translation: AAC52062.1
AF052205 mRNA Translation: AAC13273.1
AL662799 Genomic DNA No translation available.
AL021366 Genomic DNA Translation: CAA16158.1
AL021366 Genomic DNA Translation: CAA16159.1
AL050332 Genomic DNA Translation: CAC38366.1
AL050332 Genomic DNA Translation: CAC38367.1
BX088650 Genomic DNA No translation available.
CH471081 Genomic DNA Translation: EAX03729.1
CH471081 Genomic DNA Translation: EAX03730.1
BC008834 mRNA Translation: AAH08834.1
CCDSiCCDS4777.1 [O43189-1]
CCDS4778.1 [O43189-2]
RefSeqiNP_002627.1, NM_002636.4
NP_077084.1, NM_024165.2
XP_011512964.1, XM_011514662.1 [O43189-1]
UniGeneiHs.166204

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2E5PNMR-A29-83[»]
2M0ONMR-A6-83[»]
4HCZX-ray1.85A/B28-85[»]
5XFNX-ray1.90A25-340[»]
5XFOX-ray1.90A25-340[»]
5XFPX-ray2.30A/B/E25-360[»]
ProteinModelPortaliO43189
SMRiO43189
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111271, 57 interactors
DIPiDIP-34001N
IntActiO43189, 80 interactors
MINTiO43189
STRINGi9606.ENSP00000363640

Chemistry databases

BindingDBiO43189

PTM databases

iPTMnetiO43189
PhosphoSitePlusiO43189

Polymorphism and mutation databases

BioMutaiPHF1

Proteomic databases

EPDiO43189
MaxQBiO43189
PaxDbiO43189
PeptideAtlasiO43189
PRIDEiO43189
ProteomicsDBi48805
48806 [O43189-2]

Protocols and materials databases

DNASUi5252
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000374512; ENSP00000363636; ENSG00000112511 [O43189-2]
ENST00000374516; ENSP00000363640; ENSG00000112511 [O43189-1]
ENST00000427869; ENSP00000391901; ENSG00000225553
ENST00000454914; ENSP00000407295; ENSG00000225553
GeneIDi5252
KEGGihsa:5252
UCSCiuc003oeh.4 human [O43189-1]

Organism-specific databases

CTDi5252
DisGeNETi5252
EuPathDBiHostDB:ENSG00000112511.17
GeneCardsiPHF1
HGNCiHGNC:8919 PHF1
HPAiHPA031038
MIMi602881 gene
neXtProtiNX_O43189
OpenTargetsiENSG00000112511
PharmGKBiPA33259
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4323 Eukaryota
ENOG410XQ6E LUCA
GeneTreeiENSGT00390000009222
HOVERGENiHBG004755
InParanoidiO43189
KOiK11467
OMAiAPPLWDP
OrthoDBiEOG091G01JL
PhylomeDBiO43189
TreeFamiTF106420

Enzyme and pathway databases

ReactomeiR-HSA-212300 PRC2 methylates histones and DNA

Miscellaneous databases

ChiTaRSiPHF1 human
EvolutionaryTraceiO43189
GeneWikiiPHF1
GenomeRNAii5252
PROiPR:O43189
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000112511 Expressed in 232 organ(s), highest expression level in left testis
CleanExiHS_PHF1
ExpressionAtlasiO43189 baseline and differential
GenevisibleiO43189 HS

Family and domain databases

Gene3Di3.30.40.10, 1 hit
InterProiView protein in InterPro
IPR025894 Mtf2_C_dom
IPR031202 PHF1
IPR002999 Tudor
IPR019786 Zinc_finger_PHD-type_CS
IPR011011 Znf_FYVE_PHD
IPR001965 Znf_PHD
IPR019787 Znf_PHD-finger
IPR013083 Znf_RING/FYVE/PHD
PANTHERiPTHR12628:SF11 PTHR12628:SF11, 1 hit
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
PS50016 ZF_PHD_2, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPHF1_HUMAN
AccessioniPrimary (citable) accession number: O43189
Secondary accession number(s): B1AZX2
, B1AZX3, O60929, Q5SU07, Q5SU08, Q96KM7
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: January 11, 2011
Last modified: November 7, 2018
This is version 179 of the entry and version 3 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. 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
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