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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF THE YEAST GENERAL COREPRESSOR TUP1P MUTANT
 
Authors :  H. Matsumura, N. Kusaka, T. Nakamura, N. Tanaka, K. Sagegami, K. Uegaki Y. Mukai
Date :  28 Feb 12  (Deposition) - 13 Jun 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Four Helix Bundle, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Matsumura, N. Kusaka, T. Nakamura, N. Tanaka, K. Sagegami, K. Uegaki, T. Inoue, Y. Mukai
Crystal Structure Of The N-Terminal Domain Of The Yeast General Corepressor Tup1P And Its Functional Implications
J. Biol. Chem. V. 287 26528 2012
PubMed-ID: 22707714  |  Reference-DOI: 10.1074/JBC.M112.369652

(-) Compounds

Molecule 1 - GENERAL TRANSCRIPTIONAL COREPRESSOR TUP1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentN-TERMINAL DOMAIN
    GeneTUP1
    MutationYES
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainS288C
    SynonymFLOCCULATION SUPPRESSOR PROTEIN, GLUCOSE REPRESSION REGULATORY PROTEIN TUP1, REPRESSOR AER2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1DIO4Ligand/Ion1,4-DIETHYLENE DIOXIDE
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1DIO8Ligand/Ion1,4-DIETHYLENE DIOXIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:56 , VAL A:59 , TYR A:60 , ARG B:62 , HOH B:274BINDING SITE FOR RESIDUE DIO A 101
2AC2SOFTWAREARG A:62 , VAL B:59 , TYR B:60 , GLU B:63 , ARG B:67BINDING SITE FOR RESIDUE DIO B 101
3AC3SOFTWAREHIS A:66 , TYR A:73 , HIS B:66 , MET B:69 , LYS B:70 , TYR B:73 , HOH B:244BINDING SITE FOR RESIDUE DIO B 102
4AC4SOFTWARELEU A:64 , LYS A:68 , ASP A:71 , HOH A:224 , ASN B:57 , TYR B:60 , GLU B:61BINDING SITE FOR RESIDUE DIO B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VP9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VP9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VP9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3VP9)

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YCR084C1YCR084C.1III:262449-2603082142TUP1_YEAST1-7137132A:17-86
B:14-90
70
77

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:70
 aligned with TUP1_YEAST | P16649 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:70
                                    26        36        46        56        66        76        86
            TUP1_YEAST   17 DAIRQEFLQVSQEANTYRLQNQKDYDFKMNQQLAEMQQIRNTVYELELTHRKMKDAYEEEIKHLKLGLEQ 86
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:17-86 UniProt: 1-713 [INCOMPLETE]                     Transcript 1
                  3vp9 A 17 DAIRQEFLQVSQEANTYRLQNQKDYDFKMNQQLAEMQQIRNTVYERELTHRKMKDAYEEEIKHLKLGLEQ 86
                                    26        36        46        56        66        76        86

Chain B from PDB  Type:PROTEIN  Length:77
 aligned with TUP1_YEAST | P16649 from UniProtKB/Swiss-Prot  Length:713

    Alignment length:77
                                    23        33        43        53        63        73        83       
            TUP1_YEAST   14 ELLDAIRQEFLQVSQEANTYRLQNQKDYDFKMNQQLAEMQQIRNTVYELELTHRKMKDAYEEEIKHLKLGLEQRDHQ 90
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:14-90 UniProt: 1-713 [INCOMPLETE]                            Transcript 1
                  3vp9 B 14 ELLDAIRQEFLQVSQEANTYRLQNQKDYDFKMNQQLAEMQQIRNTVYERELTHRKMKDAYEEEIKHLKLGLEQRDHQ 90
                                    23        33        43        53        63        73        83       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3VP9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VP9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VP9)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TUP1_YEAST | P16649)
molecular function
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0036033    mediator complex binding    Interacting selectively and non-covalently with a mediator complex. The mediator complex is a protein complex that interacts with the carboxy-terminal domain of the largest subunit of RNA polymerase II and plays an active role in transducing the signal from a transcription factor to the transcriptional machinery. The Saccharomyces complex contains several identifiable subcomplexes: a head domain comprising Srb2, -4, and -5, Med6, -8, and -11, and Rox3 proteins; a middle domain comprising Med1, -4, and -7, Nut1 and -2, Cse2, Rgr1, Soh1, and Srb7 proteins; a tail consisting of Gal11p, Med2p, Pgd1p, and Sin4p; and a regulatory subcomplex comprising Ssn2, -3, and -8, and Srb8 proteins. Metazoan mediator complexes have similar modular structures and include homologs of yeast Srb and Med proteins.
    GO:0080025    phosphatidylinositol-3,5-bisphosphate binding    Interacting selectively and non-covalently with phosphatidylinositol-3,5-bisphosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' and 5' positions.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0001191    transcriptional repressor activity, RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, which may be a single protein or a complex, in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter. A protein binding transcription factor may or may not also interact with the template nucleic acid (either DNA or RNA) as well.
biological process
    GO:0043486    histone exchange    The replacement, within chromatin, of resident histones or histone subunits with alternative, sometimes variant, histones or subunits.
    GO:0035955    negative regulation of dipeptide transport by negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents or reduces the frequency, rate or extent of dipeptide transport by stopping, preventing or reducing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001198    negative regulation of mating-type specific transcription from RNA polymerase II promoter    Any mating-type specific process that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0000433    negative regulation of transcription from RNA polymerase II promoter by glucose    Any process involving glucose that stops, prevents or reduces the rate of transcription from an RNA polymerase II promoter.
    GO:0007070    negative regulation of transcription from RNA polymerase II promoter during mitotic cell cycle    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter that occurs during the mitotic cell cycle.
    GO:0016584    nucleosome positioning    Ordering of successions of nucleosomes into regular arrays so that nucleosomes are positioned at defined distances from one another.
    GO:2000531    regulation of fatty acid biosynthetic process by regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of the biosynthesis of fatty acids, by modulating the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:2000217    regulation of invasive growth in response to glucose limitation    Any process that modulates the frequency, rate or extent of invasive growth in response to glucose limitation.
    GO:2001020    regulation of response to DNA damage stimulus    Any process that modulates the frequency, rate or extent of response to DNA damage stimulus.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0033588    Elongator holoenzyme complex    A heterohexameric protein complex that is involved in modification of wobble nucleosides in tRNA. The complex can associate physically with hyperphosphorylated RNA polymerase II; it contains two discrete heterotrimeric subcomplexes.
    GO:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0008023    transcription elongation factor complex    Any protein complex that interacts with RNA polymerase II to increase (positive transcription elongation factor) or reduce (negative transcription elongation factor) the rate of transcription elongation.
    GO:0017053    transcriptional repressor complex    A protein complex that possesses activity that prevents or downregulates transcription.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        TUP1_YEAST | P166491erj 3vp8

(-) Related Entries Specified in the PDB File

3vp8