P31385 (DEP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Transcriptional regulatory protein DEP1

Gene names

Name:	DEP1
Synonyms:	FUN54
Ordered Locus Names:	YAL013W

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	405 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Transcription Transcription regulation
Cellular component	Cytoplasm Nucleus
Molecular function	Chromatin regulator Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone 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-dependent Inferred from electronic annotation. Source: UniProtKB-KW
Cellular_component	Rpd3L complex Inferred from direct assay PubMed 16286007Ref.9Ref.8PubMed 19040720. Source: SGD Rpd3L-Expanded complex Inferred from direct assay PubMed 19040720. Source: SGD cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 405	405	Transcriptional regulatory protein DEP1		PRO_0000079864
Regions
	Compositional bias	81 – 177	97	Glu-rich
Amino acid modifications
	Modified residue	120	1	Phosphoserine Ref.10
	Modified residue	370	1	Phosphoserine Ref.10

Sequences

	Sequence		Length	Mass (Da)
	P31385 [UniParc]. Last modified July 27, 2011. Version 3. Checksum: 3A67F052C3920A22	FASTA	405	46,978
	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

References

	« Hide 'large scale' referencesShow '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 204511 / S288c / AB972.
[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, MASS SPECTROMETRY.
+	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.
PIR	S36721.
RefSeq	NP_009389.3. NM_001178158.2.
3D structure databases
ProteinModelPortal	P31385.
SMR	P31385. Positions 174-212.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-5922N.
IntAct	P31385. 7 interactions.
MINT	MINT-641697.
STRING	4932.YAL013W.
Proteomic databases
PaxDb	P31385.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YAL013W; YAL013W; YAL013W.
GeneID	851220.
KEGG	sce:YAL013W.
Organism-specific databases
CYGD	YAL013w.
SGD	S000000011. DEP1.
Phylogenomic databases
eggNOG	NOG44093.
OrthoDB	EOG42592S.
Gene expression databases
Genevestigator	P31385.
GermOnline	YAL013W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR013907. Sds3. [Graphical view]
Pfam	PF08598. Sds3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	968115.

Entry information

Entry name

DEP1_YEAST

Accession

Primary (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:	May 1, 2013
This is version 100 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program