PHD finger protein 1 - Mus musculus (Mouse)

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Q9Z1B8 (PHF1_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 102. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	Phf1
Synonyms:	Plc1, Tctex-3, Tctex3

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	559 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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 (Ref.4). 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. Ref.4
Subunit structure	Associated component of the PRC2 complex. Interacts with p53/TP53 By similarity. Interacts with CHMP1. Ref.3
Subcellular location	Nucleus. Cytoplasm › cytoskeleton › centrosome By similarity. Note: Localizes specifically to the promoters of numerous target genes. Localizes to double-strand breaks (DSBs) sites following DNA damage. Co-localizes with NEK6 in the centrosome By similarity. Ref.4
Tissue specificity	Testis-specific.
Domain	The Tudor domain recognizes and binds H3K36me3 (Ref.5).
Sequence similarities	Belongs to the Polycomblike family. Contains 2 PHD-type zinc fingers. Contains 1 Tudor domain.

Ontologies

Keywords
Biological process	DNA damage Transcription Transcription regulation
Cellular component	Cytoplasm Cytoskeleton Nucleus
Domain	Repeat Zinc-finger
Ligand	Metal-binding Zinc
Molecular function	Chromatin regulator Repressor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin modification Inferred from electronic annotation. Source: UniProtKB-KW negative regulation of histone H3-K27 methylation Inferred from sequence or structural similarity. Source: UniProtKB positive regulation of histone H3-K27 methylation Inferred from sequence or structural similarity. Source: UniProtKB regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW response to DNA damage stimulus Inferred from sequence or structural similarity. Source: UniProtKB transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-KW microtubule organizing center Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from sequence or structural similarity. Source: UniProtKB site of double-strand break Inferred from sequence or structural similarity. Source: UniProtKB
Molecular_function	methylated histone residue binding Inferred from direct assay Ref.5. Source: UniProtKB zinc ion binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 559

559

PHD finger protein 1

PRO_0000059289

Regions

Domain

29 – 86

Tudor

Zinc finger

87 – 142

PHD-type 1

Zinc finger

186 – 240

PHD-type 2

Experimental info

Sequence conflict

249

L → F in AAD00518. Ref.2

Sequence conflict

344

G → E in BAA25074. Ref.1

Sequence conflict

377

R → S in BAA25074. Ref.1

Sequence conflict

555

G → R in BAA25074. Ref.1

Sequence conflict

558 – 559

IF → HLPDSLLLLPSPFTHWHFHA LDL in BAA25074. Ref.1

Sequences

Sequence

Length

Mass (Da)

Tools

Q9Z1B8 [UniParc].

Last modified December 1, 2000. Version 2.
Checksum: 6D2EE5F53D6164C2
Show »

FASTA

559

61,140

        10         20         30         40         50         60 
MAQLPRLSRL GAPSLWDPAS PAPTSGPRPR LWEGQDVLAR WTDGLLYLGT IKKVDSAREV 

        70         80         90        100        110        120 
CLVQFEDDSQ FLVLWKDISP AALPGEELLC CVCRSETVVP GNRLVSCEKC RHAYHQDCHV 

       130        140        150        160        170        180 
PRAPAPGEGE GASWVCRQCV FAIATKRGGA LKKGPYARAM LGMKLSLPYG LKGLDWDAGH 

       190        200        210        220        230        240 
LSNRQQSYCY CGGPGEWNLK MLQCRSCLQW FHEACTQCLS KPLLYGDRFY EFECCVCRGG 

       250        260        270        280        290        300 
PEKVRRLQLR WVDVAHLVLY HLSVCCKKKY FDFDREILPF TSENWDSLLL GELSDTPKGE 

       310        320        330        340        350        360 
RSSQLLSALN SHKDRFISGR EIKKRKCLFG LHARTPPPVE LLTGDGAPTS FPSGQGPGGG 

       370        380        390        400        410        420 
VSRPLGKRWR SEPEPLRRRQ KGKVEELGPP TAAHSRHGSR EQRALQASVS PPPPSPNQSY 

       430        440        450        460        470        480 
EGSSGYNFRP TDARCLPSSP IRMFASFHPS ASTAGTSGDS EPPDRSPLGL HIGFPTDTPK 

       490        500        510        520        530        540 
SSPHSVTASS SSVPALTPGF SRHSPPSPLC RSLSPGTGGG VRGGVSYLSR GDPVRVLARR 

       550 
VRPDGSVQYL VEWGGGGIF

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References

[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(1998) [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(1999) [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(2001) [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(2008) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[5]	"Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity." Ballare C., Lange M., Lapinaite A., Martin G.M., Morey L., Pascual G., Liefke R., Simon B., Shi Y., Gozani O., Carlomagno T., Benitah S.A., Di Croce L. Nat. Struct. Mol. Biol. 19:1257-1265(2012) [PubMed] [Europe PMC] [Abstract] Cited for: H3K36ME3-BINDING.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AB011550 mRNA. Translation: BAA25074.1. U81490 mRNA. Translation: AAD00518.1.
IPI	IPI00761860.
RefSeq	NP_033369.2. NM_009343.2.
UniGene	Mm.480590.
3D structure databases
ProteinModelPortal	Q9Z1B8.
SMR	Q9Z1B8. Positions 28-147, 190-238.
ModBase	Search...
PTM databases
PhosphoSite	Q9Z1B8.
Proteomic databases
PaxDb	Q9Z1B8.
PRIDE	Q9Z1B8.
Protocols and materials databases
DNASU	21652.
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000073724; ENSMUSP00000073402; ENSMUSG00000024193.
GeneID	21652.
KEGG	mmu:21652.
UCSC	uc008bes.1. mouse.
Organism-specific databases
CTD	5252.
MGI	MGI:98647. Phf1.
Phylogenomic databases
eggNOG	NOG244542.
GeneTree	ENSGT00390000009222.
HOGENOM	HOG000010307.
HOVERGEN	HBG004755.
InParanoid	Q9Z1B8.
KO	K11467.
OMA	SPIRMFA.
OrthoDB	EOG4SBDXN.
Gene expression databases
Bgee	Q9Z1B8.
CleanEx	MM_PHF1.
Genevestigator	Q9Z1B8.
GermOnline	ENSMUSG00000024193. Mus musculus.
Family and domain databases
Gene3D	3.30.40.10. 2 hits.
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. [Graphical view]
Pfam	PF14061. Mtf2_C. 1 hit. PF00628. PHD. 1 hit. [Graphical view]
SMART	SM00249. PHD. 2 hits. SM00333. TUDOR. 1 hit. [Graphical view]
SUPFAM	SSF57903. FYVE_PHD_ZnF. 2 hits.
PROSITE	PS50304. TUDOR. False negative. PS01359. ZF_PHD_1. 2 hits. PS50016. ZF_PHD_2. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	300920.
SOURCE	Search...

Entry information

Entry name

PHF1_MOUSE

Accession

Primary (citable) accession number: Q9Z1B8
Secondary accession number(s): O54808

Entry history

Integrated into UniProtKB/Swiss-Prot:	December 1, 2000
Last sequence update:	December 1, 2000
Last modified:	May 1, 2013
This is version 102 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Relevant documents

MGD cross-references

Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

PTM databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents