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Protein

Histone deacetylase phd1

Gene

phd1

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

Functioni

Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes (By similarity). Is not essential.By similarity

Catalytic activityi

Hydrolysis of an N(6)-acetyl-lysine residue of a histone to yield a deacetylated histone.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei158 – 1581By similarity

GO - Molecular functioni

  1. histone deacetylase activity Source: PomBase
  2. histone deacetylase activity (H4-K16 specific) Source: PomBase
  3. NAD-dependent histone deacetylase activity (H3-K14 specific) Source: UniProtKB-EC
  4. NAD-dependent histone deacetylase activity (H3-K18 specific) Source: UniProtKB-EC
  5. NAD-dependent histone deacetylase activity (H3-K9 specific) Source: UniProtKB-EC
  6. NAD-dependent histone deacetylase activity (H4-K16 specific) Source: UniProtKB-EC

GO - Biological processi

  1. chromatin remodeling Source: PomBase
  2. chromatin silencing at centromere Source: PomBase
  3. chromatin silencing at silent mating-type cassette Source: PomBase
  4. chromatin silencing at telomere Source: PomBase
  5. histone deacetylation Source: PomBase
  6. histone H4 deacetylation Source: GOC
  7. regulation of nucleosome density Source: PomBase
  8. regulation of transcription from RNA polymerase II promoter Source: PomBase
  9. transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Chromatin regulator, Hydrolase, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Names & Taxonomyi

Protein namesi
Recommended name:
Histone deacetylase phd1 (EC:3.5.1.98)
Gene namesi
Name:phd1
Synonyms:hda1
ORF Names:SPAC3G9.07c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
ProteomesiUP000002485 Componenti: Chromosome I

Organism-specific databases

PomBaseiSPAC3G9.07c.

Subcellular locationi

Nucleus Curated

GO - Cellular componenti

  1. cytoplasm Source: PomBase
  2. cytosol Source: PomBase
  3. nucleus Source: PomBase
  4. Rpd3L-Expanded complex Source: PomBase
  5. Set3 complex Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 434434Histone deacetylase phd1PRO_0000114725Add
BLAST

Proteomic databases

MaxQBiO13298.

Interactioni

Protein-protein interaction databases

BioGridi280057. 157 interactions.
MINTiMINT-4666521.
STRINGi4896.SPAC3G9.07c-1.

Structurei

3D structure databases

ProteinModelPortaliO13298.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni26 – 339314Histone deacetylaseAdd
BLAST

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000225180.
InParanoidiO13298.
KOiK11483.
OMAiDKQIHHI.
OrthoDBiEOG78M0B2.
PhylomeDBiO13298.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSiPR01270. HDASUPER.
PR01271. HISDACETLASE.

Sequencei

Sequence statusi: Complete.

O13298-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDTPETSTPY EQVEKGSFFS FRPQKKRVTY HLDEQVGNYH YGDKHPMKPH
60 70 80 90 100
RITITNHLVM GYGLHNKMSV FSPRMATFGE MSEFHREDYL DFLKRVTPDN
110 120 130 140 150
AEQFADKFQQ FNIGDDCPVF DGTYEFSQRS AGASLDASRK LVQGQTDIAI
160 170 180 190 200
NWSGGLHHAK RGEASGFCYV NDIVLAILNM LRFFPRVLYI DIDIHHGDGV
210 220 230 240 250
QQAFYESDRV LTVSFHKYNG DFFPATGNFD ENGVKGGKYF ALNVPLEDGI
260 270 280 290 300
GDEQYTSLFK SIIEPTINTF QPSAIVLQCG ADSLGYDRLG VFNLSIHAHG
310 320 330 340 350
ECVRFTRSFN IPMLVVGGGG YTLRNVARAW CYETSICVNE QIPSELPRET
360 370 380 390 400
LYYEFFAPDY TLHPRLTTKI ENKNTPKALE DLRIRALEQL RYLGGAPSVQ
410 420 430
MQQIPPDLTG HLEEEDERLN DEYLDKAVDV RVRG
Length:434
Mass (Da):49,381
Last modified:January 1, 1998 - v1
Checksum:iCA2FF0D34CA536EA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB008888 Genomic DNA. Translation: BAA23598.1.
CU329670 Genomic DNA. Translation: CAA15916.1.
PIRiT11643.
RefSeqiNP_594079.1. NM_001019506.2.

Genome annotation databases

EnsemblFungiiSPAC3G9.07c.1; SPAC3G9.07c.1:pep; SPAC3G9.07c.
GeneIDi2543643.
KEGGispo:SPAC3G9.07c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB008888 Genomic DNA. Translation: BAA23598.1.
CU329670 Genomic DNA. Translation: CAA15916.1.
PIRiT11643.
RefSeqiNP_594079.1. NM_001019506.2.

3D structure databases

ProteinModelPortaliO13298.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi280057. 157 interactions.
MINTiMINT-4666521.
STRINGi4896.SPAC3G9.07c-1.

Proteomic databases

MaxQBiO13298.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPAC3G9.07c.1; SPAC3G9.07c.1:pep; SPAC3G9.07c.
GeneIDi2543643.
KEGGispo:SPAC3G9.07c.

Organism-specific databases

PomBaseiSPAC3G9.07c.

Phylogenomic databases

eggNOGiCOG0123.
HOGENOMiHOG000225180.
InParanoidiO13298.
KOiK11483.
OMAiDKQIHHI.
OrthoDBiEOG78M0B2.
PhylomeDBiO13298.

Miscellaneous databases

NextBioi20804649.

Family and domain databases

Gene3Di3.40.800.20. 1 hit.
InterProiIPR000286. His_deacetylse.
IPR003084. His_deacetylse_1.
IPR023801. His_deacetylse_dom.
[Graphical view]
PANTHERiPTHR10625. PTHR10625. 1 hit.
PfamiPF00850. Hist_deacetyl. 1 hit.
[Graphical view]
PIRSFiPIRSF037913. His_deacetylse_1. 1 hit.
PRINTSiPR01270. HDASUPER.
PR01271. HISDACETLASE.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "phd1+, a histone deacetylase gene of Schizosaccharomyces pombe, is required for the meiotic cell cycle and resistance to trichostatin A."
    Kim Y.B., Honda A., Yoshida M., Horinouchi S.
    FEBS Lett. 436:193-196(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "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(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  3. "Genetic characterisation of hda1+, a putative fission yeast histone deacetylase gene."
    Olsson T.G.S., Ekwall K., Allshire R.C., Sunnerhagen P., Partridge J.F., Richardson W.A.
    Nucleic Acids Res. 26:3247-3254(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.

Entry informationi

Entry nameiPHD1_SCHPO
AccessioniPrimary (citable) accession number: O13298
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: January 1, 1998
Last modified: January 7, 2015
This is version 110 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

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.