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(-) Description

Title :  SOLUTION STRUCTURE OF THE SMRT DEACETYLASE ACTIVATION DOMAIN
 
Authors :  A. Codina, J. D. Love, Y. Li, M. A. Lazar, D. Neuhaus, J. W. R. Schwabe
Date :  01 Sep 04  (Deposition) - 03 May 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (28x)
Keywords :  Four-Helix Structure, Three-Helix Triangle, Transcription Corepressor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Codina, J. D. Love, Y. Li, M. A. Lazar, D. Neuhaus, J. W. R. Schwabe
Structural Insights Into The Interaction And Activation Of Histone Deacetylase 3 By Nuclear Receptor Corepressors
Proc. Natl. Acad. Sci. Usa V. 102 6009 2005
PubMed-ID: 15837933  |  Reference-DOI: 10.1073/PNAS.0500299102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR COREPRESSOR 2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPGEX-4T-1
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentDEACETYLASE ACTIVATION DOMAIN (RESIDUES 410-480)
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSMRT, N-COR2, SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR, SMRTE, THYROID-, RETINOIC- ACID-RECEPTOR-ASSOCIATED COREPRESSOR, T3 RECEPTOR- ASSOCIATING FACTOR, TRAC, CTG REPEAT PROTEIN 26, SMAP270

 Structural Features

(-) Chains, Units

  
NMR Structure (28x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1XC5)

(-) Sites  (0, 0)

(no "Site" information available for 1XC5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XC5)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SANTPS51293 SANT domain profile.NCOR2_HUMAN427-478
610-661
  1A:427-478
-

(-) Exons   (0, 0)

(no "Exon" information available for 1XC5)

(-) 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:68
 aligned with NCOR2_HUMAN | Q9Y618 from UniProtKB/Swiss-Prot  Length:2525

    Alignment length:68
                                   422       432       442       452       462       472        
          NCOR2_HUMAN   413 NGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKKNENYK 480
               SCOP domains d1xc5a1 A:413-480 Nuclear receptor corepressor 2                     SCOP domains
               CATH domains -------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------SANT  PDB: A:427-478 UniProt: 427-478               -- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1xc5 A 413 NGLMADPMKVYKDRQVMNMWSEQEKETFREKFMQHPKNFGLIASFLERKTVAECVLYYYLTKKNENYK 480
                                   422       432       442       452       462       472        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XC5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XC5)

(-) Gene Ontology  (22, 22)

NMR Structure(hide GO term definitions)
Chain A   (NCOR2_HUMAN | Q9Y618)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0016922    ligand-dependent nuclear receptor binding    Interacting selectively and non-covalently, in a ligand dependent manner, with a nuclear receptor protein.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
biological process
    GO:0044255    cellular lipid metabolic process    The chemical reactions and pathways involving lipids, as carried out by individual cells.
    GO:1903799    negative regulation of production of miRNAs involved in gene silencing by miRNA    Any process that stops, prevents or reduces the frequency, rate or extent of production of miRNAs involved in gene silencing by miRNA.
    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:0072365    regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of a cellular ketone metabolic process by stopping, preventing, or reducing 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: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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016604    nuclear body    Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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.
    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
        NCOR2_HUMAN | Q9Y6181kkq 1r2b 2gpv 2l5g 2ltp 2odd 2rt5 3r29 3r2a 4a69 4oar 5x8q 5x8x

(-) Related Entries Specified in the PDB File

6286 1H AND 15N CHEMICAL SHIFT ASSIGNMENT