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(-) Description

Title :  CRYSTAL STRUCTURE OF (H79AC102D)DTXR COMPLEXED WITH NICKEL(II)
 
Authors :  J. A. D'Aquino, D. Ringe
Date :  03 Sep 04  (Deposition) - 16 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Helix-Turn-Helix, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. D'Aquino, J. Tetenbaum-Novatt, A. White, F. Berkovitch, D. Ring
Mechanism Of Metal Ion Activation Of The Diphtheria Toxin Repressor Dtxr.
Proc. Natl. Acad. Sci. Usa V. 102 18408 2005
PubMed-ID: 16352732  |  Reference-DOI: 10.1073/PNAS.0500908102

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR MUTANT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDTXR
    MutationYES
    Organism ScientificCORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid1717
    Synonym(H79AC102D)DTXR, IRON-DEPENDENT DIPHTHERIA TOX REGULATORY ELEMENT, TOX REGULATORY FACTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (2x)A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:10 , ASP A:102 , GLU A:105 , HIS A:106BINDING SITE FOR RESIDUE NI A 252

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_DTXRPS50944 DtxR-type HTH domain profile.DTXR_CORDI4-65  1A:4-65
DTXR_CORDW4-65  1A:4-65
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HTH_DTXRPS50944 DtxR-type HTH domain profile.DTXR_CORDI4-65  2A:4-65
DTXR_CORDW4-65  2A:4-65

(-) Exons   (0, 0)

(no "Exon" information available for 1XCV)

(-) 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:139
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           DTXR_CORDI     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
               SCOP domains d1xcva1 A:1-64 Diphtheria toxin repressor (DtxR)                d1xcva2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --1xcvA01 A:3-75 'winged helix' repressor DNA binding domain               1xcvA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-1xcvA02 A:3-62                               --Fe_dep_repr_C-1xcvA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcv A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         

Chain A from PDB  Type:PROTEIN  Length:139
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           DTXR_CORDW     1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
               SCOP domains d1xcva1 A:1-64 Diphtheria toxin repressor (DtxR)                d1xcva2 A:65-139 Diphtheria toxin repressor (DtxR)                          SCOP domains
               CATH domains --1xcvA01 A:3-75 'winged helix' repressor DNA binding domain               1xcvA02 A:76-136 Diphtheria Toxin Repressor, domain 2        --- CATH domains
               Pfam domains --Fe_dep_repress-1xcvA02 A:3-62                               --Fe_dep_repr_C-1xcvA01 A:65-135                                         ---- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------H-------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ---HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           -------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xcv A   1 MKDLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKARLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         

   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  (2, 2)

Asymmetric Unit

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (7, 14)

Asymmetric Unit(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 | P0DJL71bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 2dtr 2qq9 2qqa 2qqb 2tdx 3glx
        DTXR_CORDW | H2I2331bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 2dtr 2qq9 2qqa 2qqb 2tdx 3glx

(-) Related Entries Specified in the PDB File

1p92 CRYSTAL STRUCTURE OF (H79A)DTXR
2tdx DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL