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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)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
  • metal ion binding Source: UniProtKB-KW
  • methylated histone binding Source: UniProtKB

GO - Biological processi

Keywordsi

Molecular functionChromatin regulator, Repressor
Biological processDNA damage, Transcription, Transcription regulation
LigandMetal-binding, Zinc

Enzyme and pathway databases

ReactomeiR-MMU-212300. 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 lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Chromosome 17

Organism-specific databases

MGIiMGI:98647. Phf1.

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

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000592891 – 559PHD finger protein 1Add BLAST559

Proteomic databases

MaxQBiQ9Z1B8.
PaxDbiQ9Z1B8.
PeptideAtlasiQ9Z1B8.
PRIDEiQ9Z1B8.

PTM databases

iPTMnetiQ9Z1B8.
PhosphoSitePlusiQ9Z1B8.

Expressioni

Tissue specificityi

Testis-specific.

Gene expression databases

BgeeiENSMUSG00000024193.
CleanExiMM_PHF1.
GenevisibleiQ9Z1B8. MM.

Interactioni

Subunit structurei

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

GO - Molecular functioni

  • methylated histone binding Source: UniProtKB

Protein-protein interaction databases

BioGridi204083. 2 interactors.
IntActiQ9Z1B8. 1 interactor.
MINTiMINT-4107427.
STRINGi10090.ENSMUSP00000073402.

Structurei

Secondary structure

1559
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
Beta strandi70 – 74Combined sources5
Helixi75 – 77Combined sources3
Beta strandi78 – 80Combined sources3
Turni91 – 93Combined sources3
Beta strandi104 – 106Combined sources3
Turni108 – 110Combined sources3
Beta strandi113 – 115Combined sources3
Helixi116 – 118Combined sources3
Beta strandi119 – 121Combined sources3
Beta strandi126 – 130Combined sources5
Helixi137 – 144Combined sources8
Helixi155 – 164Combined sources10
Helixi171 – 173Combined sources3
Turni189 – 191Combined sources3
Turni197 – 200Combined sources4
Beta strandi201 – 204Combined sources4
Turni205 – 207Combined sources3
Beta strandi210 – 212Combined sources3
Helixi213 – 215Combined sources3
Beta strandi230 – 233Combined sources4
Helixi235 – 238Combined sources4
Beta strandi243 – 246Combined sources4
Helixi251 – 265Combined sources15
Turni273 – 276Combined sources4
Helixi277 – 283Combined sources7
Turni285 – 288Combined sources4
Helixi291 – 293Combined sources3
Helixi298 – 311Combined sources14
Turni313 – 315Combined sources3
Beta strandi316 – 318Combined sources3
Helixi319 – 322Combined sources4
Beta strandi328 – 334Combined sources7

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5XFQX-ray2.40A/B25-360[»]
ProteinModelPortaliQ9Z1B8.
SMRiQ9Z1B8.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Domaini

The Tudor domain recognizes and binds H3K36me3.1 Publication

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.
HOGENOMiHOG000010307.
HOVERGENiHBG004755.
InParanoidiQ9Z1B8.
KOiK11467.
OMAiFGLHART.
OrthoDBiEOG091G01JL.
PhylomeDBiQ9Z1B8.
TreeFamiTF106420.

Family and domain databases

Gene3Di3.30.40.10. 2 hits.
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.

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:December 1, 2000 - v2
Checksum:i6D2EE5F53D6164C2
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti249L → F in AAD00518 (PubMed:10545244).Curated1
Sequence conflicti344G → E in BAA25074 (PubMed:9799836).Curated1
Sequence conflicti377R → S in BAA25074 (PubMed:9799836).Curated1
Sequence conflicti555G → R in BAA25074 (PubMed:9799836).Curated1
Sequence conflicti558 – 559IF → HLPDSLLLLPSPFTHWHFHA LDL in BAA25074 (PubMed:9799836).Curated2

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.2. mouse.

Similar proteinsi

Entry informationi

Entry nameiPHF1_MOUSE
AccessioniPrimary (citable) accession number: Q9Z1B8
Secondary accession number(s): O54808
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 1, 2000
Last sequence update: December 1, 2000
Last modified: November 22, 2017
This is version 141 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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