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Protein

PHD finger protein 1

Gene

PHF1

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. 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
  • methylated histone binding Source: UniProtKB
  • transcription factor activity, sequence-specific DNA binding Source: ProtInc
  • zinc ion binding Source: InterPro

GO - Biological processi

  • cellular response to DNA damage stimulus Source: UniProtKB
  • chromatin modification Source: UniProtKB-KW
  • negative regulation of gene expression, epigenetic Source: Reactome
  • negative regulation of histone H3-K27 methylation Source: UniProtKB
  • positive regulation of histone H3-K27 methylation Source: UniProtKB
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Repressor

Keywords - Biological processi

DNA damage, Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112511-MONOMER.
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

HGNCiHGNC:8919. PHF1.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: UniProtKB-KW
  • microtubule organizing center Source: UniProtKB-SubCell
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
  • site of double-strand break Source: UniProtKB
Complete GO annotation...

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.

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.

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.
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

WithEntry#Exp.IntActNotes
ATXN7L1Q9ULK23EBI-530034,EBI-310660
BIRC7Q96CA53EBI-530034,EBI-517623
CALCOCO2Q131373EBI-530034,EBI-739580
EZH2Q159104EBI-530034,EBI-530054
HSD17B14Q9BPX13EBI-530034,EBI-742664
NAB2Q157425EBI-530034,EBI-8641936
PDLIM7Q9NR123EBI-530034,EBI-350517
RBPMSQ930624EBI-530034,EBI-740322
TFCP2Q128004EBI-530034,EBI-717422
THAP1Q9NVV93EBI-530034,EBI-741515
TRIM23P364063EBI-530034,EBI-740098
VAC14Q08AM63EBI-530034,EBI-2107455

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi111271. 41 interactors.
DIPiDIP-34001N.
IntActiO43189. 54 interactors.
MINTiMINT-1437706.
STRINGi9606.ENSP00000363640.

Chemistry databases

BindingDBiO43189.

Structurei

Secondary structure

1567
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 40Combined sources5
Beta strandi46 – 55Combined sources10
Turni56 – 59Combined sources4
Beta strandi60 – 65Combined sources6
Turni66 – 68Combined sources3
Beta strandi70 – 74Combined sources5
Helixi75 – 77Combined sources3
Beta strandi78 – 80Combined sources3

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[»]
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
Contains 2 PHD-type zinc fingers.PROSITE-ProRule annotation
Contains 1 Tudor domain.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.
OMAiEMMETAG.
OrthoDBiEOG091G01JL.
PhylomeDBiO43189.
TreeFamiTF106420.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiIPR025894. 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.
[Graphical view]
PANTHERiPTHR12628:SF11. PTHR12628:SF11. 1 hit.
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.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

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

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

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_04450042T → S.Corresponds to variant rs6934613dbSNPEnsembl.1
Natural variantiVAR_034382304R → K.5 PublicationsCorresponds to variant rs3116713dbSNPEnsembl.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. Translation: CAI18271.1.
AL662799 Genomic DNA. Translation: CAI18272.1.
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. Translation: CAM26298.1.
BX088650 Genomic DNA. Translation: CAM26299.1.
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

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. Translation: CAI18271.1.
AL662799 Genomic DNA. Translation: CAI18272.1.
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. Translation: CAM26298.1.
BX088650 Genomic DNA. Translation: CAM26299.1.
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[»]
ProteinModelPortaliO43189.
SMRiO43189.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111271. 41 interactors.
DIPiDIP-34001N.
IntActiO43189. 54 interactors.
MINTiMINT-1437706.
STRINGi9606.ENSP00000363640.

Chemistry databases

BindingDBiO43189.

PTM databases

iPTMnetiO43189.
PhosphoSitePlusiO43189.

Polymorphism and mutation databases

BioMutaiPHF1.

Proteomic databases

EPDiO43189.
MaxQBiO43189.
PaxDbiO43189.
PeptideAtlasiO43189.
PRIDEiO43189.

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.
GeneCardsiPHF1.
HGNCiHGNC:8919. PHF1.
HPAiHPA031038.
MIMi602881. gene.
neXtProtiNX_O43189.
OpenTargetsiENSG00000112511.
PharmGKBiPA33259.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG4323. Eukaryota.
ENOG410XQ6E. LUCA.
GeneTreeiENSGT00390000009222.
HOVERGENiHBG004755.
InParanoidiO43189.
KOiK11467.
OMAiEMMETAG.
OrthoDBiEOG091G01JL.
PhylomeDBiO43189.
TreeFamiTF106420.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000112511-MONOMER.
ReactomeiR-HSA-212300. PRC2 methylates histones and DNA.

Miscellaneous databases

ChiTaRSiPHF1. human.
EvolutionaryTraceiO43189.
GeneWikiiPHF1.
GenomeRNAii5252.
PROiO43189.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000112511.
CleanExiHS_PHF1.
ExpressionAtlasiO43189. baseline and differential.
GenevisibleiO43189. HS.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
InterProiIPR025894. 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.
[Graphical view]
PANTHERiPTHR12628:SF11. PTHR12628:SF11. 1 hit.
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.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPHF1_HUMAN
AccessioniPrimary (citable) accession number: O43189
Secondary accession number(s): B1AZX2
, B1AZX3, O60929, Q5SU07, Q5SU08, Q96KM7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: January 11, 2011
Last modified: November 30, 2016
This is version 162 of the entry and version 3 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

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. 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.