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Protein

SWM histone demethylase complex subunit phf1

Gene

phf1

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Component of the SWM histone demethylase complex that specifically demethylates H3K9me2, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Has a role in regulating heterochromatin propagation and euchromatic transcription.2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri190 – 24657PHD-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • histone H3-K9 demethylation Source: PomBase
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
SWM histone demethylase complex subunit phf1
Alternative name(s):
PHD finger domain-containing protein phf1
Gene namesi
Name:phf1
Synonyms:saf50, swp1
ORF Names:SPCC4G3.07c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:SPCC4G3.07c.
PomBaseiSPCC4G3.07c. phf1.

Subcellular locationi

GO - Cellular componenti

  • Lsd1/2 complex Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 461461SWM histone demethylase complex subunit phf1PRO_0000363000Add
BLAST

Proteomic databases

MaxQBiP87233.

Interactioni

Subunit structurei

Component of the SWM histone demethylase complex composed of at least lsd1, lsd2, phf1 and phf2.3 Publications

Protein-protein interaction databases

BioGridi275971. 5 interactions.
MINTiMINT-4692908.

Structurei

3D structure databases

ProteinModelPortaliP87233.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Contains 1 PHD-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri190 – 24657PHD-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

InParanoidiP87233.
OrthoDBiEOG76HQ9Z.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P87233-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSQKNFFDEG KSYGVNDYAG FHFENGADSS LPQVSAQGVV RETDSSNFDA
60 70 80 90 100
SPVASGSGIS DVGPFGADFH QLQQHVQTPY GGMTMPASSS SGATSVPPEQ
110 120 130 140 150
DPSLSVSFNR LPKSASTKTK NGRIRSSRRE DDNRIPFYDL DVAEGAEDDL
160 170 180 190 200
QEDFHVEGMK TKSGRKIQRP VAYNPNATAL KRKSRKVDMV TLCSVCQRGH
210 220 230 240 250
SPLSNRIVFC DGCNSPYHQL CHHPPIDDAT VQDVDAEWFC MKCQYRRAKQ
260 270 280 290 300
PLETGMTAQD LGLSESDKKM YLSSLPTPHL ADLILFCEKS YPSLPIYNPR
310 320 330 340 350
TRELLGEIRH QLLVSSERQQ ISLQERLHAK QDEAPSDEPA PVPYTASYVA
360 370 380 390 400
NSGTLYDYPT LIRLAIRNTL SPSKDEIFNW LAQNVPLLPT FHDSASEAIR
410 420 430 440 450
WMVNKGQLVR SGSIYQIATV EEYPHLQPSL LPTFQRNRKV PKLVPVSFPT
460
DDPQNLCATV L
Length:461
Mass (Da):51,285
Last modified:July 1, 1997 - v1
Checksum:iAFCEB88216CCE1AD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAB09774.1.
PIRiT41369.
RefSeqiNP_587831.1. NM_001022824.2.

Genome annotation databases

EnsemblFungiiSPCC4G3.07c.1; SPCC4G3.07c.1:pep; SPCC4G3.07c.
GeneIDi2539406.
KEGGispo:SPCC4G3.07c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAB09774.1.
PIRiT41369.
RefSeqiNP_587831.1. NM_001022824.2.

3D structure databases

ProteinModelPortaliP87233.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275971. 5 interactions.
MINTiMINT-4692908.

Proteomic databases

MaxQBiP87233.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPCC4G3.07c.1; SPCC4G3.07c.1:pep; SPCC4G3.07c.
GeneIDi2539406.
KEGGispo:SPCC4G3.07c.

Organism-specific databases

EuPathDBiFungiDB:SPCC4G3.07c.
PomBaseiSPCC4G3.07c. phf1.

Phylogenomic databases

InParanoidiP87233.
OrthoDBiEOG76HQ9Z.

Miscellaneous databases

NextBioi20800570.
PROiP87233.

Family and domain databases

Gene3Di3.30.40.10. 1 hit.
InterProiIPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamiPF00628. PHD. 1 hit.
[Graphical view]
SMARTiSM00249. PHD. 1 hit.
[Graphical view]
SUPFAMiSSF57903. SSF57903. 1 hit.
PROSITEiPS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "Fission yeast homologs of human histone H3 lysine 4 demethylase regulate a common set of genes with diverse functions."
    Nicolas E., Lee M.G., Hakimi M.-A., Cam H.P., Grewal S.I.S., Shiekhattar R.
    J. Biol. Chem. 281:35983-35988(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX.
  3. "ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe."
    Matsuyama A., Arai R., Yashiroda Y., Shirai A., Kamata A., Sekido S., Kobayashi Y., Hashimoto A., Hamamoto M., Hiraoka Y., Horinouchi S., Yoshida M.
    Nat. Biotechnol. 24:841-847(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  4. "S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription."
    Lan F., Zaratiegui M., Villen J., Vaughn M.W., Verdel A., Huarte M., Shi Y., Gygi S.P., Moazed D., Martienssen R.A., Shi Y.
    Mol. Cell 26:89-101(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, FUNCTION OF THE SWM COMPLEX.
  5. "Genome-wide studies of histone demethylation catalysed by the fission yeast homologues of mammalian LSD1."
    Opel M., Lando D., Bonilla C., Trewick S.C., Boukaba A., Walfridsson J., Cauwood J., Werler P.J., Carr A.M., Kouzarides T., Murzina N.V., Allshire R.C., Ekwall K., Laue E.D.
    PLoS ONE 2:E386-E386(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION IN THE SWM HISTONE DEMETHYLASE COMPLEX, FUNCTION OF THE SWM COMPLEX.

Entry informationi

Entry nameiPHF1_SCHPO
AccessioniPrimary (citable) accession number: P87233
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 10, 2009
Last sequence update: July 1, 1997
Last modified: April 13, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: entries and gene names
  2. 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.