P16649 (TUP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
General transcriptional corepressor TUP1

Alternative name(s):
Flocculation suppressor protein
Glucose repression regulatory protein TUP1
Repressor AER2

Gene names

Name:	TUP1
Synonyms:	AAR1, AER2, AMM1, CYC9, FLK1, SFL2, UMR7
Ordered Locus Names:	YCR084C
ORF Names:	YCR84C

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	713 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Acts as component of the CYC8-TUP1 corepressor complex which is involved in the repression of many genes in a wide variety of physiological processes including heme-regulated and catabolite repressed genes. May also be involved in the derepression of at least some target genes. The complex is recruited to target genes by interaction with DNA-bound transcriptional repressors, like MATALPHA2, MIG1, RFX1 and SKO1. The complex recruits histone deacetylases to produce a repressive chromatin structure, interacts with hypoacetylated N-terminal tails of histones H3 and H4 that have been programmed for repression by the action of histone deacetylases and interferes directly with the transcriptional machinery by associating with the RNA polymerase II mediator complex. Ref.1 Ref.11 Ref.12 Ref.13 Ref.15 Ref.16 Ref.17
Subunit structure	Associates with CYC8/SSN6 to form the CYC8-TUP1 (or TUP1-SSN6) corepressor complex that is composed of 4 copies of TUP1 and one copy of CYC8. Interacts with histone H3, histone H4, MATALPHA2, RFX1, SKO1, PGD1, HDA1, HDA2, HOS1, HOS2 AND RPD3. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.14 Ref.15 Ref.18
Subcellular location	Nucleus Ref.19.
Miscellaneous	Present with 5840 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the WD repeat TUP1 family. Contains 7 WD repeats.
Sequence caution	The sequence CAA34411.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Domain	Repeat WD repeat
Molecular function	Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	histone exchange Inferred from mutant phenotype PubMed 17387147. Source: SGD negative regulation of dipeptide transport by negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 18708352. Source: SGD negative regulation of mating-type specific transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 1312982. Source: SGD negative regulation of transcription from RNA polymerase II promoter by glucose Inferred from mutant phenotype PubMed 9461460. Source: SGD negative regulation of transcription from RNA polymerase II promoter during mitosis Inferred from mutant phenotype PubMed 9560430. Source: SGD nucleosome positioning Inferred from direct assay PubMed 15116071. Source: SGD regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 9280286. Source: SGD regulation of response to DNA damage stimulus Inferred from mutant phenotype Ref.10. Source: SGD regulation of transcription from RNA polymerase II promoter in response to hypoxia Inferred from mutant phenotype Ref.2. Source: SGD regulation of transcription from RNA polymerase II promoter in response to osmotic stress Inferred from mutant phenotype PubMed 9858577. Source: SGD
Cellular_component	transcriptional repressor complex Inferred from direct assay PubMed 9111019. Source: SGD
Molecular_function	RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription Inferred from mutant phenotype Ref.10. Source: SGD histone deacetylase binding Inferred from direct assay Ref.18. Source: SGD mediator complex binding Inferred from direct assay PubMed 11226276. Source: SGD phosphatidylinositol-3,5-bisphosphate binding Inferred from direct assay PubMed 21536737. Source: SGD ubiquitin binding Inferred from direct assay PubMed 21070969. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CYC8	P14922	7	EBI-19654,EBI-18215
PGD1	P40356	3	EBI-19654,EBI-13268
RFX1	P48743	2	EBI-19654,EBI-15036
RPD3	P32561	2	EBI-19654,EBI-15864

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 713

713

General transcriptional corepressor TUP1

PRO_0000051312

Regions

Repeat

342 – 371

30

WD 1

Repeat

441 – 471

31

WD 2

Repeat

483 – 513

31

WD 3

Repeat

524 – 555

32

WD 4

Repeat

574 – 604

31

WD 5

Repeat

628 – 658

31

WD 6

Repeat

670 – 706

37

WD 7

Compositional bias

97 – 118

22

Gln-rich

Compositional bias

181 – 198

18

Poly-Gln

Compositional bias

399 – 409

11

Thr-rich

Amino acid modifications

Modified residue

150

1

Phosphoserine Ref.22

Modified residue

216

1

Phosphoserine Ref.22

Modified residue

218

1

Phosphothreonine Ref.22

Modified residue

253

1

Phosphoserine Ref.22

Modified residue

437

1

Phosphoserine Ref.22

Modified residue

438

1

Phosphoserine Ref.22

Modified residue

439

1

Phosphoserine Ref.21 Ref.22

Modified residue

441

1

Phosphoserine Ref.22

Modified residue

442

1

Phosphoserine Ref.22

Experimental info

Sequence conflict

75

1

E → A in AAA35182. Ref.1

Sequence conflict

100

1

R → Q in AAA35182. Ref.1

Sequence conflict

685

1

P → S in AAA35182. Ref.1

Sequence conflict

685

1

P → S in AAA34413. Ref.2

Secondary structure

1

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713

Helix Strand Turn

Details...

Turn

19 – 26

8

Helix

27 – 84

58

Beta strand

290 – 292

3

Helix

300 – 303

4

Beta strand

307 – 310

4

Beta strand

314 – 317

4

Beta strand

322 – 325

4

Beta strand

333 – 342

10

Beta strand

349 – 352

4

Beta strand

356 – 362

7

Beta strand

367 – 371

5

Turn

372 – 374

3

Beta strand

377 – 381

5

Beta strand

445 – 451

7

Beta strand

455 – 462

8

Beta strand

467 – 471

5

Turn

472 – 475

4

Beta strand

476 – 481

6

Beta strand

488 – 493

6

Beta strand

497 – 504

8

Beta strand

507 – 513

7

Turn

514 – 517

4

Beta strand

518 – 524

7

Beta strand

529 – 534

6

Beta strand

541 – 546

6

Beta strand

551 – 555

5

Turn

556 – 558

3

Beta strand

561 – 565

5

Beta strand

579 – 584

6

Beta strand

588 – 595

8

Beta strand

598 – 604

7

Beta strand

622 – 627

6

Beta strand

633 – 638

6

Helix

640 – 642

3

Beta strand

644 – 649

6

Beta strand

652 – 658

7

Turn

659 – 661

3

Beta strand

664 – 669

6

Beta strand

675 – 680

6

Beta strand

691 – 697

7

Beta strand

700 – 709

10

Sequences

	Sequence		Length	Mass (Da)
	P16649 [UniParc]. Last modified May 1, 1991. Version 2. Checksum: 444104AAD63CB944	FASTA	713	78,308
	10 20 30 40 50 60 MTASVSNTQN KLNELLDAIR QEFLQVSQEA NTYRLQNQKD YDFKMNQQLA EMQQIRNTVY 70 80 90 100 110 120 ELELTHRKMK DAYEEEIKHL KLGLEQRDHQ IASLTVQQQR QQQQQQQVQQ HLQQQQQQLA 130 140 150 160 170 180 AASASVPVAQ QPPATTSATA TPAANTTTGS PSAFPVQASR PNLVGSQLPT TTLPVVSSNA 190 200 210 220 230 240 QQQLPQQQLQ QQQLQQQQPP PQVSVAPLSN TAINGSPTSK ETTTLPSVKA PESTLKETEP 250 260 270 280 290 300 ENNNTSKIND TGSATTATTT TATETEIKPK EEDATPASLH QDHYLVPYNQ RANHSKPIPP 310 320 330 340 350 360 FLLDLDSQSV PDALKKQTND YYILYNPALP REIDVELHKS LDHTSVVCCV KFSNDGEYLA 370 380 390 400 410 420 TGCNKTTQVY RVSDGSLVAR LSDDSAANNH RNSITENNTT TSTDNNTMTT TTTTTITTTA 430 440 450 460 470 480 MTSAAELAKD VENLNTSSSP SSDLYIRSVC FSPDGKFLAT GAEDRLIRIW DIENRKIVMI 490 500 510 520 530 540 LQGHEQDIYS LDYFPSGDKL VSGSGDRTVR IWDLRTGQCS LTLSIEDGVT TVAVSPGDGK 550 560 570 580 590 600 YIAAGSLDRA VRVWDSETGF LVERLDSENE SGTGHKDSVY SVVFTRDGQS VVSGSLDRSV 610 620 630 640 650 660 KLWNLQNANN KSDSKTPNSG TCEVTYIGHK DFVLSVATTQ NDEYILSGSK DRGVLFWDKK 670 680 690 700 710 SGNPLLMLQG HRNSVISVAV ANGSPLGPEY NVFATGSGDC KARIWKYKKI APN

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Characterization of TUP1, a mediator of glucose repression in Saccharomyces cerevisiae." Williams F.E., Trumbly R.J. Mol. Cell. Biol. 10:6500-6511(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
[2]	"A yeast protein with homology to the beta-subunit of G proteins is involved in control of heme-regulated and catabolite-repressed genes." Zhang M., Rosenblum-Vos L.S., Lowry C.V., Boakye K., Zitomer R.S. Gene 97:153-161(1991) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Cloning of the yeast SFL2 gene: its disruption results in pleiotropic phenotypes characteristic for tup1 mutants." Fujita A., Matsumoto S., Kuhara S., Misumi Y., Kobayashi H. Gene 89:93-99(1990) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 44774 / DBY747.
[4]	"The complete DNA sequence of yeast chromosome III." Oliver S.G., van der Aart Q.J.M., Agostoni-Carbone M.L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J.P.G., Benit P., Berben G., Bergantino E., Biteau N., Bolle P.-A., Bolotin-Fukuhara M., Brown A., Brown A.J.P., Buhler J.-M. , Carcano C., Carignani G., Cederberg H., Chanet R., Contreras R., Crouzet M., Daignan-Fornier B., Defoor E., Delgado M.D., Demolder J., Doira C., Dubois E., Dujon B., Duesterhoeft A., Erdmann D., Esteban M., Fabre F., Fairhead C., Faye G., Feldmann H., Fiers W., Francingues-Gaillard M.-C., Franco L., Frontali L., Fukuhara H., Fuller L.J., Galland P., Gent M.E., Gigot D., Gilliquet V., Glansdorff N., Goffeau A., Grenson M., Grisanti P., Grivell L.A., de Haan M., Haasemann M., Hatat D., Hoenicka J., Hegemann J.H., Herbert C.J., Hilger F., Hohmann S., Hollenberg C.P., Huse K., Iborra F., Indge K.J., Isono K., Jacq C., Jacquet M., James C.M., Jauniaux J.-C., Jia Y., Jimenez A., Kelly A., Kleinhans U., Kreisl P., Lanfranchi G., Lewis C., van der Linden C.G., Lucchini G., Lutzenkirchen K., Maat M.J., Mallet L., Mannhaupt G., Martegani E., Mathieu A., Maurer C.T.C., McConnell D., McKee R.A., Messenguy F., Mewes H.-W., Molemans F., Montague M.A., Muzi Falconi M., Navas L., Newlon C.S., Noone D., Pallier C., Panzeri L., Pearson B.M., Perea J., Philippsen P., Pierard A., Planta R.J., Plevani P., Poetsch B., Pohl F.M., Purnelle B., Ramezani Rad M., Rasmussen S.W., Raynal A., Remacha M.A., Richterich P., Roberts A.B., Rodriguez F., Sanz E., Schaaff-Gerstenschlaeger I., Scherens B., Schweitzer B., Shu Y., Skala J., Slonimski P.P., Sor F., Soustelle C., Spiegelberg R., Stateva L.I., Steensma H.Y., Steiner S., Thierry A., Thireos G., Tzermia M., Urrestarazu L.A., Valle G., Vetter I., van Vliet-Reedijk J.C., Voet M., Volckaert G., Vreken P., Wang H., Warmington J.R., von Wettstein D., Wicksteed B.L., Wilson C., Wurst H., Xu G., Yoshikawa A., Zimmermann F.K., Sgouros J.G. Nature 357:38-46(1992) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[6]	"The SFL2 (TUP1?) protein of Saccharomyces cerevisiae contains a repeating motif homologous to beta subunits of G proteins." Kearsley S. Gene 98:147-148(1991) [PubMed] [Europe PMC] [Abstract] Cited for: SIMILARITY TO BETA SUBUNIT OF G-PROTEINS.
[7]	"The WD repeats of Tup1 interact with the homeo domain protein alpha 2." Komachi K., Redd M.J., Johnson A.D. Genes Dev. 8:2857-2867(1994) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH MATALPHA2.
[8]	"Repression domain of the yeast global repressor Tup1 interacts directly with histones H3 and H4." Edmondson D.G., Smith M.M., Roth S.Y. Genes Dev. 10:1247-1259(1996) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HISTONE H3 AND HISTONE H4.
[9]	"The Cyc8 (Ssn6)-Tup1 corepressor complex is composed of one Cyc8 and four Tup1 subunits." Varanasi U.S., Klis M., Mikesell P.B., Trumbly R.J. Mol. Cell. Biol. 16:6707-6714(1996) [PubMed] [Europe PMC] [Abstract] Cited for: SUBUNIT.
[10]	"The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor." Huang M., Zhou Z., Elledge S.J. Cell 94:595-605(1998) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH RFX1.
[11]	"Ssn6-Tup1 interacts with class I histone deacetylases required for repression." Watson A.D., Edmondson D.G., Bone J.R., Mukai Y., Yu Y., Du W., Stillman D.J., Roth S.Y. Genes Dev. 14:2737-2744(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH CYC8 AND RPD3, FUNCTION OF THE CYC8-TUP1 COMPLEX.
[12]	"Hrs1/Med3 is a Cyc8-Tup1 corepressor target in the RNA polymerase II holoenzyme." Papamichos-Chronakis M., Conlan R.S., Gounalaki N., Copf T., Tzamarias D. J. Biol. Chem. 275:8397-8403(2000) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH PGD1, FUNCTION OF THE CYC8-TUP1 COMPLEX.
[13]	"Regulation of the Sko1 transcriptional repressor by the Hog1 MAP kinase in response to osmotic stress." Proft M., Pascual-Ahuir A., de Nadal E., Arino J., Serrano R., Posas F. EMBO J. 20:1123-1133(2001) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE CYC8-TUP1 COMPLEX.
[14]	"Multiple levels of control regulate the yeast cAMP-response element-binding protein repressor Sko1p in response to stress." Pascual-Ahuir A., Posas F., Serrano R., Proft M. J. Biol. Chem. 276:37373-37378(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH SKO1.
[15]	"TUP1 utilizes histone H3/H2B-specific HDA1 deacetylase to repress gene activity in yeast." Wu J., Suka N., Carlson M., Grunstein M. Mol. Cell 7:117-126(2001) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HDA1 AND HDA2, FUNCTION OF THE CYC8-TUP1 COMPLEX.
[16]	"Histone-dependent association of Tup1-Ssn6 with repressed genes in vivo." Davie J.K., Trumbly R.J., Dent S.Y. Mol. Cell. Biol. 22:693-703(2002) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE CYC8-TUP1 COMPLEX.
[17]	"Recruitment of Tup1-Ssn6 by yeast hypoxic genes and chromatin-independent exclusion of TATA binding protein." Mennella T.A., Klinkenberg L.G., Zitomer R.S. Eukaryot. Cell 2:1288-1303(2003) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION OF THE CYC8-TUP1 COMPLEX.
[18]	"Tup1-Ssn6 interacts with multiple class I histone deacetylases in vivo." Davie J.K., Edmondson D.G., Coco C.B., Dent S.Y. J. Biol. Chem. 278:50158-50162(2003) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH HOS1; HOS2 AND RPD3.
[19]	"Global analysis of protein localization in budding yeast." Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K. Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract] Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[20]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[21]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-439, MASS SPECTROMETRY. Strain: YAL6B.
[22]	"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-150; SER-216; THR-218; SER-253; SER-437; SER-438; SER-439; SER-441 AND SER-442, MASS SPECTROMETRY.
[23]	"Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast." Sprague E.R., Redd M.J., Johnson A.D., Wolberger C. EMBO J. 19:3016-3027(2000) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 282-713.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M31733 Genomic DNA. Translation: AAA35182.1.
M35861 Genomic DNA. Translation: AAA34413.1.
X16365 Genomic DNA. Translation: CAA34411.1. Different initiation.
X59720 Genomic DNA. Translation: CAA42259.1.
BK006937 Genomic DNA. Translation: DAA07554.1.

PIR

JN0133.

RefSeq

NP_010007.1. NM_001178790.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ERJ	X-ray	2.30	A/B/C	282-713	[»]
3VP8	X-ray	1.91	A/B/C/D	1-92	[»]
3VP9	X-ray	1.80	A/B	1-92	[»]

ProteinModelPortal

P16649.

SMR

P16649. Positions 2-81, 283-710.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-512N.

IntAct

P16649. 22 interactions.

MINT

MINT-648551.

Proteomic databases

PaxDb

P16649.

PeptideAtlas

P16649.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YCR084C; YCR084C; YCR084C.

GeneID

850445.

KEGG

sce:YCR084C.

Organism-specific databases

CYGD

YCR084c.

SGD

S000000680. TUP1.

Phylogenomic databases

eggNOG

COG2319.

GeneTree

ENSGT00700000104507.

HOGENOM

HOG000200558.

KO

K06666.

OMA

TISESCI.

OrthoDB

EOG4KM2C2.

Gene expression databases

Genevestigator

P16649.

GermOnline

YCR084C. Saccharomyces cerevisiae.

Family and domain databases

Gene3D

2.130.10.10. 2 hits.

InterPro

IPR020472. G-protein_beta_WD-40_rep.
IPR013890. Tscrpt_rep_Tup1_N.
IPR015943. WD40/YVTN_repeat-like_dom.
IPR001680. WD40_repeat.
IPR019775. WD40_repeat_CS.
IPR017986. WD40_repeat_dom.
[Graphical view]

Pfam

PF08581. Tup_N. 1 hit.
PF00400. WD40. 7 hits.
[Graphical view]

PRINTS

PR00320. GPROTEINBRPT.

ProDom

PD010558. Transcrip_repressor_Tup1_N. 1 hit.
[Graphical view] [Entries sharing at least one domain]

SMART

SM00320. WD40. 7 hits.
[Graphical view]

SUPFAM

SSF50978. WD40_like. 1 hit.

PROSITE

PS00678. WD_REPEATS_1. 4 hits.
PS50082. WD_REPEATS_2. 5 hits.
PS50294. WD_REPEATS_REGION. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P16649.

NextBio

966057.

Entry information

Entry name

TUP1_YEAST

Accession

Primary (citable) accession number: P16649
Secondary accession number(s): D6VR85, P17995, P18323

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	May 1, 1991
Last modified:	May 1, 2013
This is version 146 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program