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(-) Description

Title :  C TERMINAL SH3-LIKE DOMAIN FROM DIPHTHERIA TOXIN REPRESSOR RESIDUES 144-226.
 
Authors :  G. P. Wylie, V. Rangachari, E. A. Bienkiewicz, V. Marin, N. Bhattacharya, J. F. Love, J. R. Murphy, T. M. Logan
Date :  28 Aug 03  (Deposition) - 02 Nov 04  (Release) - 21 Apr 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (13x)
Keywords :  Repressor, Dtxr, C-Terminal Domain, Prokaryotic Sh3 Domain, Transcription Regulation, Peptide-Binding, Gene Regulation, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. P. Wylie, V. Rangachari, E. A. Bienkiewicz, V. Marin, N. Bhattacharya, J. F. Love, J. R. Murphy, T. M. Logan
Prolylpeptide Binding By The Prokaryotic Sh3-Like Domain Of The Diphtheria Toxin Repressor: A Regulatory Switch.
Biochemistry V. 44 40 2005
PubMed-ID: 15628844  |  Reference-DOI: 10.1021/BI048035P
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PET-15B
    Fragment: RESIDUES 144-226
    Gene: DTXR
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717
    Synonym: IRON-DEPENDENT DIPHTHERIA TOX REGULATORY ELEMENT, TOX REGULATORY FACTOR

 Structural Features

(-) Chains, Units

  
NMR Structure (13x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1QVP)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

NMR Structure (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_002 *G141RDTXR_CORDI  ---  ---AS141R
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 1QVP)

(-) Exons   (0, 0)

(no "Exon" information available for 1QVP)

(-) 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:87
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:98
                                   138       148       158       168       178       188       198       208       218        
           DTXR_CORDI   129 GNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d           1qvpa_ A: Diphtheria toxin repressor (DtxR)                                            SCOP domains
               CATH domains 1           qvpA00 A:140-226  [code=2.30.30.90, no name defined]                                   CATH domains
               Pfam domains --------------------------FeoA-1qvpA01 A:155-225                                                 - Pfam domains
         Sec.struct. author .-----------.....................eeeeee........hhhhhhhhhh......eeeeee....eeeee..eee..........eee.. 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
                 1qvp A 140 G-----------SHMDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                            |        -  |    148       158       168       178       188       198       208       218        
                            |         141                                                                                     
                          140                                                                                                 


Chain A from PDB  Type:PROTEIN  Length:87
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:98
                                   138       148       158       168       178       188       198       208       218        
           DTXR_CORDW   129 GNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d           1qvpa_ A: Diphtheria toxin repressor (DtxR)                                            SCOP domains
               CATH domains 1           qvpA00 A:140-226  [code=2.30.30.90, no name defined]                                   CATH domains
               Pfam domains --------------------------FeoA-1qvpA01 A:155-225                                                 - Pfam domains
         Sec.struct. author .-----------.....................eeeeee........hhhhhhhhhh......eeeeee....eeeee..eee..........eee.. 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
                 1qvp A 140 G-----------SHMDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
                            |        -  |    148       158       168       178       188       198       208       218        
                          140         141
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: TRB (15)

(-) Gene Ontology  (7, 14)

NMR Structure(hide GO term definitions)
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.

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DTXR_CORDI | P0DJL7: 1bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx
        DTXR_CORDW | H2I233: 1bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx 3glx

(-) Related Entries Specified in the PDB File

7998 CHEMICAL SHIFTS FOR THIS ENTRY
1bym PDB FILE FOR THE C TERMINAL DOMAIN OF THIS SAME PROTEIN RESIDUES 130-226