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(-) Description

Title :  SOLUTION STRUCTURES OF THE C-TERMINAL DOMAIN OF DIPHTHERIA TOXIN REPRESSOR
 
Authors :  G. Wang, G. P. Wylie, P. D. Twigg, D. L. D. Caspar, J. R. Murphy, T. M. Logan
Date :  17 Oct 98  (Deposition) - 21 Oct 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Repressor, Dtxr, C-Terminal Domain, Prokaryotic Sh3 Domain, Transcription Regulation, Peptide-Binding, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Wang, G. P. Wylie, P. D. Twigg, D. L. Caspar, J. R. Murphy, T. M. Logan
Solution Structure And Peptide Binding Studies Of The C-Terminal Src Homology 3-Like Domain Of The Diphtheria Toxin Repressor Protein.
Proc. Natl. Acad. Sci. Usa V. 96 6119 1999
PubMed-ID: 10339551  |  Reference-DOI: 10.1073/PNAS.96.11.6119
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (DIPHTHERIA TOXIN REPRESSOR)
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainHMS-174
    Expression System Taxid562
    Expression System VectorPQE-31
    FragmentRESIDUES 130-226
    GeneDTXR
    Organism ScientificCORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid1717
    Other DetailsSWS P33120
    SynonymDTXR(130-226)

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1BYM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

NMR Structure (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_002 *G141RDTXR_CORDI  ---  ---AG141R
02UniProtVAR_DTXR_CORDI_003 *V147ADTXR_CORDI  ---  ---AA147A
03UniProtVAR_DTXR_CORDI_004 *I165VDTXR_CORDI  ---  ---AI165V
04UniProtVAR_DTXR_CORDI_005 *V174ADTXR_CORDI  ---  ---AV174A
05UniProtVAR_DTXR_CORDI_006 *S191TDTXR_CORDI  ---  ---AS191T
06UniProtVAR_DTXR_CORDI_007 *D199VDTXR_CORDI  ---  ---AD199V
07UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
08UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
09UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
10UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
11UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
12UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
13UniProtVAR_DTXR_CORDI_014 *I221TDTXR_CORDI  ---  ---AI221T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1BYM)

(-) 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:97
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:97
                                   139       149       159       169       179       189       199       209       219       
           DTXR_CORDI   130 NPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d1byma_ A: Diphtheria toxin repressor (DtxR)                                                      SCOP domains
               CATH domains 1bymA00 A:130-226  [code=2.30.30.90, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhh........eeeee.........hhhhhhhhh.......eeeeee..eeeeee..eee...hhhh...eeee. Sec.struct. author
             SAPs(SNPs) (1) -----------R-----A-----------------V--------A----------------T-------V-R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1bym A 130 NPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                                   139       149       159       169       179       189       199       209       219       

Chain A from PDB  Type:PROTEIN  Length:97
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:97
                                   139       149       159       169       179       189       199       209       219       
           DTXR_CORDW   130 NPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d1byma_ A: Diphtheria toxin repressor (DtxR)                                                      SCOP domains
               CATH domains 1bymA00 A:130-226  [code=2.30.30.90, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................hhhh........eeeee.........hhhhhhhhh.......eeeeee..eeeeee..eee...hhhh...eeee. Sec.struct. author
             SAPs(SNPs) (1) -----------R-----A-----------------V--------A----------------T-------V-R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 1bym A 130 NPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                                   139       149       159       169       179       189       199       209       219       

   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  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 14)

NMR Structure(hide GO term definitions)
Chain A   (DTXR_CORDW | H2I233)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A   (DTXR_CORDI | P0DJL7)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DTXR_CORDI | P0DJL71bi0 1bi1 1bi2 1bi3 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx
        DTXR_CORDW | H2I2331bi0 1bi1 1bi2 1bi3 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx

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