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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL WD40 DOMAIN OF SIF2
 
Authors :  D. Cerna, D. K. Wilson
Date :  10 Oct 03  (Deposition) - 01 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription Corepressor, Wd40 Repeat, Beta Propeller (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Cerna, D. K. Wilson
The Structure Of Sif2P, A Wd Repeat Protein Functioning In The Set3 Corepressor Complex.
J. Mol. Biol. V. 351 923 2005
PubMed-ID: 16051270  |  Reference-DOI: 10.1016/J.JMB.2005.06.025
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SIR4-INTERACTING PROTEIN SIF2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PTYB2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL WD40 DOMAIN (RESIDUES 113-535)
    Gene: SIF2
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:179 , ARG A:183 , ARG A:207 , HOH A:2183BINDING SITE FOR RESIDUE SO4 A 1001
2AC2SOFTWARETHR A:164 , SER A:513 , HOH A:2014 , HOH A:2052 , HOH A:2065 , HOH A:2231 , HOH A:2250BINDING SITE FOR RESIDUE SO4 A 1002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R5M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R5M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R5M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R5M)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YBR103W1YBR103W.1II:447703-4493101608SIF2_YEAST1-5355351A:146-535 (gaps)390

(-) Sequences/Alignments

Asymmetric/Biological 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:351
 aligned with SIF2_YEAST | P38262 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:392
                                                                                                                                                                                                                                                                                                                                                                                                                               535  
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535  
           SIF2_YEAST   146 GFVKILKEIVKLDNIVSSTWNPLDESILAYGEKNSVARLARIVETDQEGKKYWKLTIIAELRHPFALSASSGKTTNQVTCLAWSHDGNSIVTGVENGELRLWNKTGALLNVLNFHRAPIVSVKWNKDGTHIISMDVENVTILWNVISGTVMQHFELKETGGSSINAENHSGDGSLGVDVEWVDDDKFVIPGPKGAIFVYQITEKTPTGKLIGHHGPISVLEFNDTNKLLLSASDDGTLRIWHGGNGNSQNCFYGHSQSIVSASWVGDDKVISCSMDGSVRLWSLKQNTLLALSIVDGVPIFAGRISQDGQKYAVAFMDGQVNVYDLKKLNSKSRSLYGNRDGILNPLPIPLYASYQSSQDNDYIFDLSWNCAGNKISVAYSLQEGSVVAI--   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 1r5mA00 A:146-537 YVTN repeat-like/Quinoprote      in amine dehydrog      enase                                                                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1r5mA01 A:391-428                ------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1r5mA02 A:391-428                ------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------WD40-1r5mA03 A:391-428                ------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ...ee.eeeee.....eeee......eeeeee...eeeeeeee..------..eeeeeeeee......------...eeeeee.....eeeeee....eeeee....eeeee......eeeeee.....eeeeee....eeeee....eeeeee...---------------.......eeee..eeeee.hhh.eeeee.......eee......eeeeeee....eeeeee....eeee........eee......eeeeeee...eeeeee...eeeeee....eeeeeee.....eeeeee.....eeeeee....eeeeehhhhhh--------------.ee..eeeee........eeeeee.....eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:146-535 (gaps) UniProt: 1-535 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                           -- Transcript 1
                 1r5m A 146 GFVKILKEIVKLDNIVSSTWNPLDESILAYGEKNSVARLARIVET------YWKLTIIAELRHPFALS------TNQVTCLAWSHDGNSIVTGVENGELRLWNKTGALLNVLNFHRAPIVSVKWNKDGTHIISMDVENVTILWNVISGTVMQHFELK---------------GSLGVDVEWVDDDKFVIPGPKGAIFVYQITEKTPTGKLIGHHGPISVLEFNDTNKLLLSASDDGTLRIWHGGNGNSQNCFYGHSQSIVSASWVGDDKVISCSMDGSVRLWSLKQNTLLALSIVDGVPIFAGRISQDGQKYAVAFMDGQVNVYDLKKLNS--------------PLPIPLYASYQSSQDNDYIFDLSWNCAGNKISVAYSLQEGSVVAIPG 537
                                   155       165       175       185    |    - |     205       | -    |  225       235       245       255       265       275       285       295      |  -         -  |    325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475|        -     | 495       505       515       525       535  
                                                                      190    197             213    220                                                                               302             318                                                                                                                                                           476            491
   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 1R5M)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Beta_propeller (192)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SIF2_YEAST | P38262)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0031939    negative regulation of chromatin silencing at telomere    Any process that stops, prevents, or reduces the frequency, rate or extent of chromatin silencing at telomeres.
    GO:0045835    negative regulation of meiotic nuclear division    Any process that stops, prevents, or reduces the frequency, rate or extent of meiosis.
    GO:1903507    negative regulation of nucleic acid-templated transcription    Any process that stops, prevents or reduces the frequency, rate or extent of nucleic acid-templated transcription.
    GO:0032874    positive regulation of stress-activated MAPK cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0034967    Set3 complex    A histone deacetylase complex that is involved in transcriptional regulation. In S. cerevisiae, this complex consists of Set3p, Snt1p, Hos4p, Sif2p, Cpr1p, Hos2p, and Hst1p.
    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.

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