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Protein

PHD finger protein 1

Gene

Phf1

Organism
Mus musculus (Mouse)
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:18086877). According to other reports, PHF1 recruits the PRC2 complex at double-strand breaks (DSBs) and inhibits the activity of PRC2. Regulates p53/TP53 stability and prolonges its turnover: may act by specifically binding to a methylated from of p53/TP53.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri87 – 14256PHD-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri186 – 24055PHD-type 2PROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

  1. methylated histone binding Source: UniProtKB
  2. zinc ion binding Source: InterPro

GO - Biological processi

  1. cellular response to DNA damage stimulus Source: UniProtKB
  2. chromatin modification Source: UniProtKB-KW
  3. negative regulation of histone H3-K27 methylation Source: UniProtKB
  4. positive regulation of histone H3-K27 methylation Source: UniProtKB
  5. regulation of transcription, DNA-templated Source: UniProtKB-KW
  6. 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

ReactomeiREACT_298576. PRC2 methylates histones and DNA.

Names & Taxonomyi

Protein namesi
Recommended name:
PHD finger protein 1
Short name:
Protein PHF1
Alternative name(s):
Polycomb-like protein 1
Short name:
mPCl1
T-complex testis-expressed 3
Gene namesi
Name:Phf1
Synonyms:Plc1, Tctex-3, Tctex3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 17

Organism-specific databases

MGIiMGI:98647. Phf1.

Subcellular locationi

Nucleus 1 Publication. Cytoplasmcytoskeletonmicrotubule organizing centercentrosome By similarity
Note: Localizes specifically to the promoters of numerous target genes. Localizes to double-strand breaks (DSBs) sites following DNA damage. Colocalizes with NEK6 in the centrosome (By similarity).By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-KW
  2. ESC/E(Z) complex Source: Ensembl
  3. microtubule organizing center Source: UniProtKB-SubCell
  4. nucleoplasm Source: MGI
  5. nucleus Source: UniProtKB
  6. site of double-strand break Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Cytoskeleton, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 559559PHD finger protein 1PRO_0000059289Add
BLAST

Proteomic databases

PaxDbiQ9Z1B8.
PRIDEiQ9Z1B8.

PTM databases

PhosphoSiteiQ9Z1B8.

Expressioni

Tissue specificityi

Testis-specific.

Gene expression databases

BgeeiQ9Z1B8.
CleanExiMM_PHF1.
GenevestigatoriQ9Z1B8.

Interactioni

Subunit structurei

Associated component of the PRC2 complex. Interacts with p53/TP53 (By similarity). Interacts with CHMP1.By similarity1 Publication

Protein-protein interaction databases

BioGridi204083. 2 interactions.
IntActiQ9Z1B8. 1 interaction.
MINTiMINT-4107427.

Structurei

3D structure databases

ProteinModelPortaliQ9Z1B8.
SMRiQ9Z1B8. Positions 28-147.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini29 – 8658TudorAdd
BLAST

Domaini

The Tudor domain recognizes and binds H3K36me3.1 Publication

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)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri87 – 14256PHD-type 1PROSITE-ProRule annotationAdd
BLAST
Zinc fingeri186 – 24055PHD-type 2PROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiNOG244542.
GeneTreeiENSGT00390000009222.
HOGENOMiHOG000010307.
HOVERGENiHBG004755.
InParanoidiQ9Z1B8.
KOiK11467.
OMAiGEPPDRS.
OrthoDBiEOG73V6JJ.
PhylomeDBiQ9Z1B8.
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.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9Z1B8-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAQLPRLSRL GAPSLWDPAS PAPTSGPRPR LWEGQDVLAR WTDGLLYLGT
60 70 80 90 100
IKKVDSAREV CLVQFEDDSQ FLVLWKDISP AALPGEELLC CVCRSETVVP
110 120 130 140 150
GNRLVSCEKC RHAYHQDCHV PRAPAPGEGE GASWVCRQCV 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
RSSQLLSALN SHKDRFISGR EIKKRKCLFG LHARTPPPVE LLTGDGAPTS
360 370 380 390 400
FPSGQGPGGG VSRPLGKRWR SEPEPLRRRQ KGKVEELGPP TAAHSRHGSR
410 420 430 440 450
EQRALQASVS PPPPSPNQSY EGSSGYNFRP TDARCLPSSP IRMFASFHPS
460 470 480 490 500
ASTAGTSGDS EPPDRSPLGL HIGFPTDTPK SSPHSVTASS SSVPALTPGF
510 520 530 540 550
SRHSPPSPLC RSLSPGTGGG VRGGVSYLSR GDPVRVLARR VRPDGSVQYL

VEWGGGGIF
Length:559
Mass (Da):61,140
Last modified:November 30, 2000 - v2
Checksum:i6D2EE5F53D6164C2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti249 – 2491L → F in AAD00518 (PubMed:10545244).Curated
Sequence conflicti344 – 3441G → E in BAA25074 (PubMed:9799836).Curated
Sequence conflicti377 – 3771R → S in BAA25074 (PubMed:9799836).Curated
Sequence conflicti555 – 5551G → R in BAA25074 (PubMed:9799836).Curated
Sequence conflicti558 – 5592IF → HLPDSLLLLPSPFTHWHFHA LDL in BAA25074 (PubMed:9799836).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011550 mRNA. Translation: BAA25074.1.
U81490 mRNA. Translation: AAD00518.1.
CCDSiCCDS37518.1.
RefSeqiNP_033369.2. NM_009343.3.
UniGeneiMm.258953.

Genome annotation databases

EnsembliENSMUST00000073724; ENSMUSP00000073402; ENSMUSG00000024193.
GeneIDi21652.
KEGGimmu:21652.
UCSCiuc008bes.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB011550 mRNA. Translation: BAA25074.1.
U81490 mRNA. Translation: AAD00518.1.
CCDSiCCDS37518.1.
RefSeqiNP_033369.2. NM_009343.3.
UniGeneiMm.258953.

3D structure databases

ProteinModelPortaliQ9Z1B8.
SMRiQ9Z1B8. Positions 28-147.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi204083. 2 interactions.
IntActiQ9Z1B8. 1 interaction.
MINTiMINT-4107427.

PTM databases

PhosphoSiteiQ9Z1B8.

Proteomic databases

PaxDbiQ9Z1B8.
PRIDEiQ9Z1B8.

Protocols and materials databases

DNASUi21652.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000073724; ENSMUSP00000073402; ENSMUSG00000024193.
GeneIDi21652.
KEGGimmu:21652.
UCSCiuc008bes.1. mouse.

Organism-specific databases

CTDi5252.
MGIiMGI:98647. Phf1.

Phylogenomic databases

eggNOGiNOG244542.
GeneTreeiENSGT00390000009222.
HOGENOMiHOG000010307.
HOVERGENiHBG004755.
InParanoidiQ9Z1B8.
KOiK11467.
OMAiGEPPDRS.
OrthoDBiEOG73V6JJ.
PhylomeDBiQ9Z1B8.
TreeFamiTF106420.

Enzyme and pathway databases

ReactomeiREACT_298576. PRC2 methylates histones and DNA.

Miscellaneous databases

NextBioi300920.
PROiQ9Z1B8.
SOURCEiSearch...

Gene expression databases

BgeeiQ9Z1B8.
CleanExiMM_PHF1.
GenevestigatoriQ9Z1B8.

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.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Tctex3, related to Drosophila polycomblike, is expressed in male germ cells and mapped to the mouse T-complex."
    Kawakami S., Mitsunaga K., Kikuti Y.Y., Ando A., Inoko H., Yamamura K., Abe K.
    Mamm. Genome 9:874-880(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Tissue: Testis.
  2. "Misexpression of Polycomb-group proteins in Xenopus alters anterior neural development and represses neural target genes."
    Yoshitake Y., Howard T.L., Christian J.L., Hollenberg S.M.
    Dev. Biol. 215:375-387(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: NIH Swiss.
  3. "CHMP1 is a novel nuclear matrix protein affecting chromatin structure and cell-cycle progression."
    Stauffer D.R., Howard T.L., Nyun T., Hollenberg S.M.
    J. Cell Sci. 114:2383-2393(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH CHMP1.
  4. "Role of hPHF1 in H3K27 methylation and Hox gene silencing."
    Cao R., Wang H., He J., Erdjument-Bromage H., Tempst P., Zhang Y.
    Mol. Cell. Biol. 28:1862-1872(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.
  5. Cited for: H3K36ME3-BINDING.

Entry informationi

Entry nameiPHF1_MOUSE
AccessioniPrimary (citable) accession number: Q9Z1B8
Secondary accession number(s): O54808
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 30, 2000
Last sequence update: November 30, 2000
Last modified: March 31, 2015
This is version 120 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.