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(-) Description

Title :  CTBP/BARS IN TERNARY COMPLEX WITH NAD(H) AND PIDLSKK PEPTIDE
 
Authors :  M. Nardini, S. Spano, C. Cericola, A. Pesce, A. Massaro, E. Millo, A. Lui D. Corda, M. Bolognesi
Date :  13 Mar 03  (Deposition) - 19 Jun 03  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Trancription Co-Repressor, Transcription Co-Repression, Acyltransferase, Brefeldin A, Nad, Golgi Membrane, Acyl-Coa (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Nardini, S. Spano, C. Cericola, A. Pesce, A. Massaro, E. Millo, A. Luini, D. Corda, M. Bolognesi
Ctbp/Bars: A Dual-Function Protein Involved In Transcription Co-Repression And Golgi Membrane Fission
Embo J. V. 22 3122 2003
PubMed-ID: 12805226  |  Reference-DOI: 10.1093/EMBOJ/CDG283
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-TERMINAL BINDING PROTEIN 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11D-HIS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentRESIDUES 1-350
    OrganBRAIN
    Organism CommonRAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymCTBP3
 
Molecule 2 - PRO-ILE-ASP-LEU-SER-LYS-LYS PEPTIDE
    ChainsB
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630
    SyntheticYES

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NAD1Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NAD2Ligand/IonNICOTINAMIDE-ADENINE-DINUCLEOTIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:89 , THR A:117 , GLY A:170 , GLY A:172 , ARG A:173 , VAL A:174 , TYR A:192 , ASP A:193 , PRO A:194 , TYR A:195 , HIS A:225 , CYS A:226 , GLY A:227 , ASN A:229 , ASN A:232 , THR A:253 , ALA A:254 , ARG A:255 , ASP A:279 , VAL A:280 , HIS A:304 , TRP A:307BINDING SITE FOR RESIDUE NAD A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1HL3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:284 -Pro A:285
2Ile A:332 -Pro A:333

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1HL3)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.CTBP1_RAT166-193  1A:166-193
2D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.CTBP1_RAT244-260  1A:244-260
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_2_HYDROXYACID_DH_1PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.CTBP1_RAT166-193  2A:166-193
2D_2_HYDROXYACID_DH_3PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.CTBP1_RAT244-260  2A:244-260

(-) Exons   (0, 0)

(no "Exon" information available for 1HL3)

(-) 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:332
 aligned with CTBP1_RAT | Q9Z2F5 from UniProtKB/Swiss-Prot  Length:430

    Alignment length:332
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344  
            CTBP1_RAT    15 PRPLVALLDGRDCTVEMPILKDVATVAFCDAQSTQEIHEKVLNEAVGALMYHTITLTREDLEKFKALRIIVRIGSGFDNIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRTTWLHQALREGTRVQSVEQIREVASGAARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGIERALGLQRVSTLQDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQGPLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGRIPDSLKNCVNKDHLT 346
               SCOP domains d1hl3a2 A:15-114,A:308-346 Transcription corepressor CtbP                                           d1hl3a1 A:115-307 Transcription corepressor CtbP                                                                                                                                                 d1hl3a2 A:15-114,A:308-346              SCOP domains
               CATH domains -1hl3A01 A:16-113,A:308-341 NAD(P)-binding Rossmann-like Domain                                    1hl3A02 A:114-307 NAD(P)-binding Rossmann-like Domain                                                                                                                                             1hl3A01 A:16-113,A:308-341        ----- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee........hhhhhh...eeee.........hhhhhhh..eeee......hhhhhh......eeee........hhhhhhhh..eeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh..........eeee..hhhhhhhhhhhhhh....eee......hhhhhhh.ee..hhhhhhhhh.eeee............hhhhhhh.....eeee..hhhh.hhhhhhhhhhhh...eeee............hhhhhh..eee.......hhhhhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------D_2_HYDROXYACID_DH_1        --------------------------------------------------D_2_HYDROXYACID_D-------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hl3 A  15 PRPLVALLDGRDCTVEMPILKDVATVAFCDAQSTQEIHEKVLNEAVGALMYHTITLTREDLEKFKALRIIVRIGSGFDNIDIKSAGDLGIAVCNVPAASVEETADSTLCHILNLYRRTTWLHQALREGTRVQSVEQIREVASGAARIRGETLGIIGLGRVGQAVALRAKAFGFNVLFYDPYLSDGIERALGLQRVSTLQDLLFHSDCVTLHCGLNEHNHHLINDFTVKQMRQGAFLVNTARGGLVDEKALAQALKEGRIRGAALDVHESEPFSFSQGPLKDAPNLICTPHAAWYSEQASIEMREEAAREIRRAITGRIPDSLKNCVNKDHLT 346
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344  

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .ee.... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 1hl3 B   1 PIDLSKK   7

   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  (2, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HL3)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (CTBP1_RAT | Q9Z2F5)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0061025    membrane fusion    The membrane organization process that joins two lipid bilayers to form a single membrane.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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.
    GO:0050872    white fat cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a white adipocyte, an animal connective tissue cell involved in energy storage. White adipocytes have cytoplasmic lipids arranged in a unique vacuole.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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

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UniProtKB/Swiss-Prot
        CTBP1_RAT | Q9Z2F51hku 2hu2 3ga0

(-) Related Entries Specified in the PDB File

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