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P31385 (DEP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 107. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Transcriptional regulatory protein DEP1
Gene names
Name:DEP1
Synonyms:FUN54
Ordered Locus Names:YAL013W
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length405 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Component of the RPD3C(L) histone deacetylase complex (HDAC) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Ref.7

Subunit structure

Component of the RPD3C(L) complex composed of at least ASH1, CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. Ref.8 Ref.9

Subcellular location

Cytoplasm. Nucleus.

Sequence caution

The sequence AAC04944.2 differs from that shown. Reason: Frameshift at position 405.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentCytoplasm
Nucleus
   Molecular functionChromatin regulator
Repressor
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processhistone deacetylation

Inferred from mutant phenotype PubMed 16286007Ref.9Ref.8. Source: SGD

negative regulation of chromatin silencing at rDNA

Inferred from mutant phenotype Ref.9. Source: SGD

negative regulation of chromatin silencing at silent mating-type cassette

Inferred from mutant phenotype Ref.9. Source: SGD

negative regulation of chromatin silencing at telomere

Inferred from direct assay PubMed 20133733. Source: SGD

negative regulation of inositol biosynthetic process by negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

negative regulation of phosphatidylcholine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

negative regulation of phosphatidylserine biosynthetic process by negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

positive regulation of inositol biosynthetic process by positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

positive regulation of phosphatidylcholine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

positive regulation of phosphatidylserine biosynthetic process by positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

positive regulation of transcription from RNA polymerase II promoter in response to heat stress

Inferred from mutant phenotype PubMed 20398213. Source: SGD

regulation of DNA-dependent DNA replication initiation

Inferred from mutant phenotype PubMed 19417103. Source: SGD

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentRpd3L complex

Inferred from direct assay PubMed 16286007Ref.9Ref.8. Source: SGD

cytoplasm

Inferred from electronic annotation. Source: UniProtKB-SubCell

intermediate filament

Inferred from electronic annotation. Source: InterPro

   Molecular_functionstructural molecule activity

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 405405Transcriptional regulatory protein DEP1
PRO_0000079864

Regions

Compositional bias81 – 17797Glu-rich

Amino acid modifications

Modified residue561Phosphoserine Ref.11
Modified residue1201Phosphoserine Ref.10 Ref.11
Modified residue3701Phosphoserine Ref.10

Sequences

Sequence LengthMass (Da)Tools
P31385 [UniParc].

Last modified July 27, 2011. Version 3.
Checksum: 3A67F052C3920A22

FASTA40546,978
        10         20         30         40         50         60 
MSQQTPQESE QTTAKEQDLD QESVLSNIDF NTDLNHNLNL SEYCISSDAG TEKMDSDEEK 

        70         80         90        100        110        120 
SLANLPELKY APKLSSLVKQ ETLTESLKRP HEDEKEAIDE AKKMKVPGEN EDESKEEEKS 

       130        140        150        160        170        180 
QELEEAIDSK EKSTDARDEQ GDEGDNEEEN NEEDNENENE HTAPPALVMP SPIEMEEQRM 

       190        200        210        220        230        240 
TALKEITDIE YKFAQLRQKL YDNQLVRLQT ELQMCLEGSH PELQVYYSKI AAIRDYKLHR 

       250        260        270        280        290        300 
AYQRQKYELS CINTETIATR TFIHQDFHKK VTDLRARLLN RTTQTWYDIN KERRDMDIVI 

       310        320        330        340        350        360 
PDVNYHVPIK LDNKTLSCIT GYASAAQLCY PGEPVAEDLA CESIEYRYRA NPVDKLEVIV 

       370        380        390        400 
DRMRLNNEIS DLEGLRKYFH SFPGAPELNP LRDSEINDDF HQWAQ 

« Hide

References

« Hide 'large scale' references
[1]"Sequencing of chromosome I from Saccharomyces cerevisiae: analysis of a 32 kb region between the LTE1 and SPO7 genes."
Ouellette B.F.F., Clark M.W., Keng T., Storms R.K., Zhong W.-W., Zeng B., Fortin N., Delaney S., Barton A.B., Kaback D.B., Bussey H.
Genome 36:32-42(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204511 / S288c / AB972.
[2]"Molecular cloning of chromosome I DNA from Saccharomyces cerevisiae: analysis of the genes in the FUN38-MAK16-SPO7 region."
Barton A.B., Kaback D.B.
J. Bacteriol. 176:1872-1880(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"The nucleotide sequence of chromosome I from Saccharomyces cerevisiae."
Bussey H., Kaback D.B., Zhong W.-W., Vo D.H., Clark M.W., Fortin N., Hall J., Ouellette B.F.F., Keng T., Barton A.B., Su Y., Davies C.J., Storms R.K.
Proc. Natl. Acad. Sci. U.S.A. 92:3809-3813(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Sethuraman A., Cherry J.M.
Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases
Cited for: SEQUENCE REVISION TO C-TERMINUS.
[5]Saccharomyces Genome Database
Submitted (MAR-2011) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION, SEQUENCE REVISION TO 405.
Strain: ATCC 204508 / S288c.
[6]"Reinvestigation of the Saccharomyces cerevisiae genome annotation by comparison to the genome of a related fungus: Ashbya gossypii."
Brachat S., Dietrich F.S., Voegeli S., Zhang Z., Stuart L., Lerch A., Gates K., Gaffney T.D., Philippsen P.
Genome Biol. 4:R45.1-R45.13(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 302-361.
Strain: ATCC 204511 / S288c / AB972.
[7]"Isolation and characterization of a mutant of Saccharomyces cerevisiae with pleiotropic deficiencies in transcriptional activation and repression."
Lamping E., Lueckl J., Paltauf F., Henry S.A., Kohlwein S.D.
Genetics 137:55-65(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Stable incorporation of sequence specific repressors Ash1 and Ume6 into the Rpd3L complex."
Carrozza M.J., Florens L., Swanson S.K., Shia W.-J., Anderson S., Yates J., Washburn M.P., Workman J.L.
Biochim. Biophys. Acta 1731:77-87(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE RPD3C(L) COMPLEX, MASS SPECTROMETRY.
[9]"Cotranscriptional set2 methylation of histone H3 lysine 36 recruits a repressive Rpd3 complex."
Keogh M.-C., Kurdistani S.K., Morris S.A., Ahn S.H., Podolny V., Collins S.R., Schuldiner M., Chin K., Punna T., Thompson N.J., Boone C., Emili A., Weissman J.S., Hughes T.R., Strahl B.D., Grunstein M., Greenblatt J.F., Buratowski S., Krogan N.J.
Cell 123:593-605(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE RPD3C(L) COMPLEX, MASS SPECTROMETRY.
[10]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-120 AND SER-370, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-56 AND SER-120, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L05146 Genomic DNA. Translation: AAC04944.2. Frameshift.
AY260888 Genomic DNA. Translation: AAP21756.1.
BK006935 Genomic DNA. Translation: DAA06975.2.
PIRS36721.
RefSeqNP_009389.3. NM_001178158.2.

3D structure databases

ProteinModelPortalP31385.
SMRP31385. Positions 174-212.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31753. 461 interactions.
DIPDIP-5922N.
IntActP31385. 7 interactions.
MINTMINT-641697.
STRING4932.YAL013W.

Proteomic databases

PaxDbP31385.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYAL013W; YAL013W; YAL013W.
GeneID851220.
KEGGsce:YAL013W.

Organism-specific databases

CYGDYAL013w.
SGDS000000011. DEP1.

Phylogenomic databases

eggNOGNOG44093.
OrthoDBEOG7CK3H7.

Enzyme and pathway databases

BioCycYEAST:G3O-28825-MONOMER.

Gene expression databases

GenevestigatorP31385.

Family and domain databases

InterProIPR001664. IF.
IPR013907. Sds3.
[Graphical view]
PANTHERPTHR23239. PTHR23239. 1 hit.
PfamPF08598. Sds3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio968115.

Entry information

Entry nameDEP1_YEAST
AccessionPrimary (citable) accession number: P31385
Secondary accession number(s): D6VPK5, Q86ZS5
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 27, 2011
Last modified: March 19, 2014
This is version 107 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome I

Yeast (Saccharomyces cerevisiae) chromosome I: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD