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PDBsum entry 1erj
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Transcription inhibitor PDB id
1erj

 

 

 

 

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Contents
Protein chains
350 a.a. *
Waters ×265
* Residue conservation analysis
PDB id:
1erj
Name: Transcription inhibitor
Title: Crystal structure of thE C-terminal wd40 domain of tup1
Structure: Transcriptional repressor tup1. Chain: a, b, c. Fragment: c-terminal wd40 domain (residues 389 to 431 deleted). Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.30Å     R-factor:   0.228     R-free:   0.266
Authors: E.R.Sprague,M.J.Redd,A.D.Johnson,C.Wolberger
Key ref:
E.R.Sprague et al. (2000). Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast. EMBO J, 19, 3016-3027. PubMed id: 10856245 DOI: 10.1093/emboj/19.12.3016
Date:
06-Apr-00     Release date:   26-Jul-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16649  (TUP1_YEAST) -  General transcriptional corepressor TUP1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Seq:
Struc: 		 
Seq:
Struc: 		713 a.a.
350 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1093/emboj/19.12.3016 EMBO J 19:3016-3027 (2000)
PubMed id: 10856245  
 
 
Structure of the C-terminal domain of Tup1, a corepressor of transcription in yeast.
E.R.Sprague, M.J.Redd, A.D.Johnson, C.Wolberger.
 
  ABSTRACT  
 
The Tup1-Ssn6 corepressor complex regulates the expression of several sets of genes, including genes that specify mating type in the yeast Saccharomyces cerevisiae. Repression of mating-type genes occurs when Tup1-Ssn6 is brought to the DNA by the Matalpha2 DNA-binding protein and assembled upstream of a- and haploid-specific genes. We have determined the 2.3 A X-ray crystal structure of the C-terminal domain of Tup1 (accesion No. 1ERJ), a 43 kDa fragment that contains seven copies of the WD40 sequence motif and binds to the Matalpha2 protein. Moreover, this portion of the protein can partially substitute for full-length Tup1 in bringing about transcriptional repression. The structure reveals a seven-bladed beta propeller with an N-terminal subdomain that is anchored to the side of the propeller and extends the beta sheet of one of the blades. Point mutations in Tup1 that specifically affect the Tup1-Matalpha2 interaction cluster on one surface of the propeller. We identified regions of Tup1 that are conserved among the fungal Tup1 homologs and may be important in protein-protein interactions with additional components of the Tup1-mediated repression pathways.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 Packing of the N-terminal fragment against the propeller. (A) Extended sheet formed by blade 6 and strands n1 and n2 from the N-terminal fragment. Hydrogen bonds are indicated with dashed lines. (B) Stereoview of contacts between the N-terminal fragment (283–331) and the propeller. Side chain and backbone atoms are superimposed on the C[ ]trace. Some side chain labels were omitted for clarity. The approximate boundaries of each blade are shown in different colors (blade 5, light green; blade 6, blue; blade 7, red; N-terminal fragment, gray). This figure was generated with RIBBONS (Carson, 1997). 		Figure 3.
Figure 3 (A) Superposition of all seven blades of Tup1. The C[ ]backbone for each of the seven blades was aligned with respect to strands 3B and 3C. The four conserved side chains involved in the intrablade hydrogen-bonding network, referred to as the structural tetrad, are shown for blade 3 as ball-and-stick models colored according to atom type and hydrogen bonds are indicated with dashed lines. A representative blade from G , blade 4, is shown for reference. Blade 1, light green; blade 2, red; blade 3, green; blade 4, purple; blade 5, pink; blade 6, cyan; blade 7, orange; G , brown. (B) Superposition of the WD40 propellers. The C[ ]backbones for G (blue; 1TBG) and Tup1 (yellow), which align with an r.m.s.d. of 1.3 Å, are shown in the same view as Figure 1A and labeled. Least-squares alignments for (A) and (B) were done in O (Jones et al., 1991) and figures generated with RIBBONS (Carson, 1997).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3016-3027) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20820861 M.Lamas-Maceiras, M.A.Freire-Picos, and A.M.Torres (2011).
Transcriptional repression by Kluyveromyces lactis Tup1 in Saccharomyces cerevisiae.
  J Ind Microbiol Biotechnol, 38, 79-84.  
20459612 D.Chevanne, S.J.Saupe, C.Clavé, and M.Paoletti (2010).
WD-repeat instability and diversification of the Podospora anserina hnwd non-self recognition gene family.
  BMC Evol Biol, 10, 134.  
20544037 M.E.Ferreira, K.D.Berndt, J.Nilsson, and A.P.Wright (2010).
WD40 domain divergence is important for functional differences between the fission yeast Tup11 and Tup12 co-repressor proteins.
  PLoS One, 5, e11009.  
18424510 B.W.Kebaara, M.L.Langford, D.H.Navarathna, R.Dumitru, K.W.Nickerson, and A.L.Atkin (2008).
Candida albicans Tup1 is involved in farnesol-mediated inhibition of filamentous-growth induction.
  Eukaryot Cell, 7, 980-987.  
18061494 H.Liu, D.Abramczyk, C.R.Cooper, L.Zheng, C.Park, and P.J.Szaniszlo (2008).
Molecular cloning and characterization of WdTUP1, a gene that encodes a potential transcriptional repressor important for yeast-hyphal transitions in Wangiella (Exophiala) dermatitidis.
  Fungal Genet Biol, 45, 646-656.  
18715992 H.Ullah, E.L.Scappini, A.F.Moon, L.V.Williams, D.L.Armstrong, and L.C.Pedersen (2008).
Structure of a signal transduction regulator, RACK1, from Arabidopsis thaliana.
  Protein Sci, 17, 1771-1780.
PDB code: 3dm0
18611861 M.Buscarlet, A.Perin, A.Laing, J.M.Brickman, and S.Stifani (2008).
Inhibition of Cortical Neuron Differentiation by Groucho/TLE1 Requires Interaction with WRPW, but Not Eh1, Repressor Peptides.
  J Biol Chem, 283, 24881-24888.  
  19204818 N.V.Valeyev, A.K.Downing, J.Sondek, and C.Deane (2008).
Electrostatic and Functional Analysis of the Seven-Bladed WD beta-Propellers.
  Evol Bioinform Online, 4, 203-216.  
18483215 T.Suganuma, S.G.Pattenden, and J.L.Workman (2008).
Diverse functions of WD40 repeat proteins in histone recognition.
  Genes Dev, 22, 1265-1268.  
17356694 M.Paoletti, S.J.Saupe, and C.Clavé (2007).
Genesis of a fungal non-self recognition repertoire.
  PLoS ONE, 2, e283.  
17937914 V.Srinivasan, D.J.Netz, H.Webert, J.Mascarenhas, A.J.Pierik, H.Michel, and R.Lill (2007).
Structure of the yeast WD40 domain protein Cia1, a component acting late in iron-sulfur protein biogenesis.
  Structure, 15, 1246-1257.
PDB code: 2hes
17937919 Z.Han, X.Xing, M.Hu, Y.Zhang, P.Liu, and J.Chai (2007).
Structural basis of EZH2 recognition by EED.
  Structure, 15, 1306-1315.
PDB code: 2qxv
16829959 A.J.Ruthenburg, W.Wang, D.M.Graybosch, H.Li, C.D.Allis, D.J.Patel, and G.L.Verdine (2006).
Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex.
  Nat Struct Mol Biol, 13, 704-712.
PDB codes: 2cnx 2co0 2h68 2h6k 2h6n 2h6q
17052456 A.Mylona, C.Fernández-Tornero, P.Legrand, M.Haupt, A.Sentenac, J.Acker, and C.W.Müller (2006).
Structure of the tau60/Delta tau91 subcomplex of yeast transcription factor IIIC: insights into preinitiation complex assembly.
  Mol Cell, 24, 221-232.
PDB code: 2j04
16950773 D.A.Palmer, J.K.Thompson, L.Li, A.Prat, and P.Wang (2006).
Gib2, a novel Gbeta-like/RACK1 homolog, functions as a Gbeta subunit in cAMP signaling and is essential in Cryptococcus neoformans.
  J Biol Chem, 281, 32596-32605.  
16272155 K.Naylor, E.Ingerman, V.Okreglak, M.Marino, J.E.Hinshaw, and J.Nunnari (2006).
Mdv1 interacts with assembled dnm1 to promote mitochondrial division.
  J Biol Chem, 281, 2177-2183.  
16936817 T.M.Malavé, and S.Y.Dent (2006).
Transcriptional repression by Tup1-Ssn6.
  Biochem Cell Biol, 84, 437-443.  
15644329 D.K.Wilson, D.Cerna, and E.Chew (2005).
The 1.1-angstrom structure of the spindle checkpoint protein Bub3p reveals functional regions.
  J Biol Chem, 280, 13944-13951.
PDB code: 1yfq
15632072 F.Fagerström-Billai, and A.P.Wright (2005).
Functional comparison of the Tup11 and Tup12 transcriptional corepressors in fission yeast.
  Mol Cell Biol, 25, 716-727.  
16314508 J.Balk, D.J.Aguilar Netz, K.Tepper, A.J.Pierik, and R.Lill (2005).
The essential WD40 protein Cia1 is involved in a late step of cytosolic and nuclear iron-sulfur protein assembly.
  Mol Cell Biol, 25, 10833-10841.  
15800061 J.Gatfield, I.Albrecht, B.Zanolari, M.O.Steinmetz, and J.Pieters (2005).
Association of the leukocyte plasma membrane with the actin cytoskeleton through coiled coil-mediated trimeric coronin 1 molecules.
  Mol Biol Cell, 16, 2786-2798.  
16204884 L.J.Beamer, X.Li, C.A.Bottoms, and M.Hannink (2005).
Conserved solvent and side-chain interactions in the 1.35 Angstrom structure of the Kelch domain of Keap1.
  Acta Crystallogr D Biol Crystallogr, 61, 1335-1342.
PDB code: 1zgk
15788561 S.R.Green, and A.D.Johnson (2005).
Genome-wide analysis of the functions of a conserved surface on the corepressor Tup1.
  Mol Biol Cell, 16, 2605-2613.  
15152089 A.Y.Madrona, and D.K.Wilson (2004).
The structure of Ski8p, a protein regulating mRNA degradation: Implications for WD protein structure.
  Protein Sci, 13, 1557-1565.
PDB code: 1sq9
15103630 J.Liu, and B.Rost (2004).
CHOP proteins into structural domain-like fragments.
  Proteins, 55, 678-688.  
15039343 K.Campbell, V.Popov, and L.Soong (2004).
Identification and molecular characterization of a gene encoding a protective Leishmania amazonensis Trp-Asp (WD) protein.
  Infect Immun, 72, 2194-2202.  
14983005 K.Ginalski, L.Rychlewski, D.Baker, and N.V.Grishin (2004).
Protein structure prediction for the male-specific region of the human Y chromosome.
  Proc Natl Acad Sci U S A, 101, 2305-2310.  
14871953 S.Pöggeler, and U.Kück (2004).
A WD40 repeat protein regulates fungal cell differentiation and can be replaced functionally by the mammalian homologue striatin.
  Eukaryot Cell, 3, 232-240.  
14668334 S.Znaidi, B.Pelletier, Y.Mukai, and S.Labbé (2004).
The Schizosaccharomyces pombe corepressor Tup11 interacts with the iron-responsive transcription factor Fep1.
  J Biol Chem, 279, 9462-9474.  
15340168 Z.Cheng, Y.Liu, C.Wang, R.Parker, and H.Song (2004).
Crystal structure of Ski8p, a WD-repeat protein with dual roles in mRNA metabolism and meiotic recombination.
  Protein Sci, 13, 2673-2684.
PDB code: 1s4u
12958590 C.A.Love, K.Harlos, N.Mavaddat, S.J.Davis, D.I.Stuart, E.Y.Jones, and R.M.Esnouf (2003).
The ligand-binding face of the semaphorins revealed by the high-resolution crystal structure of SEMA4D.
  Nat Struct Biol, 10, 843-848.
PDB code: 1olz
12820959 G.Wu, G.Xu, B.A.Schulman, P.D.Jeffrey, J.W.Harper, and N.P.Pavletich (2003).
Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity of the SCF(beta-TrCP1) ubiquitin ligase.
  Mol Cell, 11, 1445-1456.
PDB code: 1p22
14593203 J.Zhang, N.Zheng, and P.Zhou (2003).
Exploring the functional complexity of cellular proteins by protein knockout.
  Proc Natl Acad Sci U S A, 100, 14127-14132.  
14517324 K.L.Cerveny, and R.E.Jensen (2003).
The WD-repeats of Net2p interact with Dnm1p and Fis1p to regulate division of mitochondria.
  Mol Biol Cell, 14, 4126-4139.  
14561773 T.A.Edwards, B.D.Wilkinson, R.P.Wharton, and A.K.Aggarwal (2003).
Model of the brain tumor-Pumilio translation repressor complex.
  Genes Dev, 17, 2508-2513.
PDB code: 1q7f
12807914 W.C.Voegtli, A.Y.Madrona, and D.K.Wilson (2003).
The structure of Aip1p, a WD repeat protein that regulates Cofilin-mediated actin depolymerization.
  J Biol Chem, 278, 34373-34379.
PDB codes: 1pgu 1pi6
12637515 Y.Mukai, J.K.Davie, and S.Y.Dent (2003).
Physical and functional interaction of the yeast corepressor Tup1 with mRNA 5'-triphosphatase.
  J Biol Chem, 278, 18895-18901.  
11781871 A.M.Motley, P.Brites, L.Gerez, E.Hogenhout, J.Haasjes, R.Benne, H.F.Tabak, R.J.Wanders, and H.R.Waterham (2002).
Mutational spectrum in the PEX7 gene and functional analysis of mutant alleles in 78 patients with rhizomelic chondrodysplasia punctata type 1.
  Am J Hum Genet, 70, 612-624.  
12100480 C.Zhang, D.Wu-Scharf, B.R.Jeong, and H.Cerutti (2002).
A WD40-repeat containing protein, similar to a fungal co-repressor, is required for transcriptional gene silencing in Chlamydomonas.
  Plant J, 31, 25-36.  
  12019224 E.Espagne, P.Balhadère, M.L.Penin, C.Barreau, and B.Turcq (2002).
HET-E and HET-D belong to a new subfamily of WD40 proteins involved in vegetative incompatibility specificity in the fungus Podospora anserina.
  Genetics, 161, 71-81.  
12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
12057191 L.M.Pickles, S.M.Roe, E.J.Hemingway, S.Stifani, and L.H.Pearl (2002).
Crystal structure of the C-terminal WD40 repeat domain of the human Groucho/TLE1 transcriptional corepressor.
  Structure, 10, 751-761.
PDB code: 1gxr
12325024 N.Braverman, L.Chen, P.Lin, C.Obie, G.Steel, P.Douglas, P.K.Chakraborty, J.T.Clarke, A.Boneh, A.Moser, H.Moser, and D.Valle (2002).
Mutation analysis of PEX7 in 60 probands with rhizomelic chondrodysplasia punctata and functional correlations of genotype with phenotype.
  Hum Mutat, 20, 284-297.  
11937049 Z.Jawad, and M.Paoli (2002).
Novel sequences propel familiar folds.
  Structure, 10, 447-454.  
  12136003 Z.Zhang, U.Varanasi, and R.J.Trumbly (2002).
Functional dissection of the global repressor Tup1 in yeast: dominant role of the C-terminal repression domain.
  Genetics, 161, 957-969.  
11250134 C.L.Woodcock, and S.Dimitrov (2001).
Higher-order structure of chromatin and chromosomes.
  Curr Opin Genet Dev, 11, 130-135.  
11551928 F.Gori, P.Divieti, and M.B.Demay (2001).
Cloning and characterization of a novel WD-40 repeat protein that dramatically accelerates osteoblastic differentiation.
  J Biol Chem, 276, 46515-46522.  
11731482 J.S.Dasen, J.P.Barbera, T.S.Herman, S.O.Connell, L.Olson, B.Ju, J.Tollkuhn, S.H.Baek, D.W.Rose, and M.G.Rosenfeld (2001).
Temporal regulation of a paired-like homeodomain repressor/TLE corepressor complex and a related activator is required for pituitary organogenesis.
  Genes Dev, 15, 3193-3207.  
11226162 M.Holm, C.S.Hardtke, R.Gaudet, and X.W.Deng (2001).
Identification of a structural motif that confers specific interaction with the WD40 repeat domain of Arabidopsis COP1.
  EMBO J, 20, 118-127.  
11054826 A.Blasco, and P.Sanz (2000).
Current awareness on yeast.
  Yeast, 16, 1449-1456.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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