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(-) Description

Title :  SOLUTION STRUCTURE OF THE SAP30 ZINC FINGER MOTIF
 
Authors :  Y. He, R. Imhoff, A. Sahu, I. Radhakrishnan
Date :  14 Jan 09  (Deposition) - 17 Mar 09  (Release) - 12 May 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (47x)
Keywords :  Sap30, Sin3, Zinc Finger Motif, Nucleic Acid Interaction, Nucleus, Repressor, Transcription, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. He, R. Imhoff, A. Sahu, I. Radhakrishnan
Solution Structure Of A Novel Zinc Finger Motif In The Sap30 Polypeptide Of The Sin3 Corepressor Complex And Its Potential Role In Nucleic Acid Recognition
Nucleic Acids Res. V. 37 2142 2009
PubMed-ID: 19223330  |  Reference-DOI: 10.1093/NAR/GKP051
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE COMPLEX SUBUNIT SAP30
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PMCSG7
    Gene: SAP30
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SIN3-ASSOCIATED POLYPEPTIDE, 30 KDA, SIN3 COREPRESSOR COMPLEX SUBUNIT SAP30

 Structural Features

(-) Chains, Units

  
NMR Structure (47x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:67 , LEU A:69 , CYS A:76 , ARG A:78 , CYS A:112BINDING SITE FOR RESIDUE ZN A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2KDP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2KDP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2KDP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2KDP)

(-) Exons   (0, 0)

(no "Exon" information available for 2KDP)

(-) Sequences/Alignments

NMR Structure
   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:71
 aligned with SAP30_HUMAN | O75446 from UniProtKB/Swiss-Prot  Length:220

    Alignment length:81
                                    60        70        80        90       100       110       120       130 
          SAP30_HUMAN    51 SAAGPPGAAGPGPGQLCCLREDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSARHLYICDYHKNLIQSVRNRRKRKGS 131
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------zf-SAP30-2kdpA01 A:65-131                                           Pfam domains
         Sec.struct. author ....----------....eee...............hhhhhhhhhh...eee..........hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2kdp A  61 SNAG----------QLCCLREDGERCGRAAGNASFSKRIQKSISQKKVKIELDKSARHLYICDYHKNLIQSVRNRRKRKGS 131
                               |     -    |   70        80        90       100       110       120       130 
                              64         65
   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 2KDP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KDP)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: zf-SAP30] (1)

(-) Gene Ontology  (13, 13)

NMR Structure(hide GO term definitions)
Chain A   (SAP30_HUMAN | O75446)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0035914    skeletal muscle cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a skeletal muscle cell, a somatic cell located in skeletal muscle.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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