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(-) Description

Title :  CRYSTAL STRUCTURE OF DTXR(D6A C102D) COMPLEXED WITH NICKEL(II)
 
Authors :  J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe
Date :  26 Jul 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Repressor, Regulator, Dtxr, Helix-Turn-Helix, Metal Ion, Activation, Dna-Binding, Ferrous Iron, Transcription, Transcription Regulation, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. D'Aquino, J. R. Lattimer, A. Denninger, K. E. D'Aquino, D. Ringe
Role Of The N-Terminal Helix In The Metal Ion-Induced Activation Of The Diphtheria Toxin Repressor Dtxr.
Biochemistry V. 46 11761 2007
PubMed-ID: 17902703  |  Reference-DOI: 10.1021/BI7007883

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL-21(DE3)
    Expression System Taxid469008
    GeneDTXR
    MutationYES
    Organism ScientificCORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid1717
    SynonymIRON-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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1NI2Ligand/IonNICKEL (II) ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , PO4 A:600 , HOH A:629 , HOH A:642BINDING SITE FOR RESIDUE NI A 551
2AC2SOFTWAREMET A:10 , ASP A:102 , GLU A:105 , HIS A:106 , HOH A:616BINDING SITE FOR RESIDUE NI A 552
3AC3SOFTWAREHIS A:79 , ARG A:80 , GLU A:83 , SER A:126 , PHE A:128 , ASN A:130 , NI A:551 , HOH A:629 , HOH A:642BINDING SITE FOR RESIDUE PO4 A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QQ9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1His A:201 -Ile A:202
2Glu A:225 -Leu A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
02UniProtVAR_DTXR_CORDI_004 *I165VDTXR_CORDI  ---  ---AI165V
03UniProtVAR_DTXR_CORDI_005 *V174ADTXR_CORDI  ---  ---AV174A
04UniProtVAR_DTXR_CORDI_006 *S191TDTXR_CORDI  ---  ---AS191T
05UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
06UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
07UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
08UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
09UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
10UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
11UniProtVAR_DTXR_CORDI_014 *I221TDTXR_CORDI  ---  ---AI221T
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (11, 22)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_DTXR_CORDI_001 *R47HDTXR_CORDI  ---  ---AR47H
02UniProtVAR_DTXR_CORDI_004 *I165VDTXR_CORDI  ---  ---AI165V
03UniProtVAR_DTXR_CORDI_005 *V174ADTXR_CORDI  ---  ---AV174A
04UniProtVAR_DTXR_CORDI_006 *S191TDTXR_CORDI  ---  ---AS191T
05UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
06UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
07UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
08UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
09UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
10UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
11UniProtVAR_DTXR_CORDI_014 *I221TDTXR_CORDI  ---  ---AI221T
   * 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 2QQ9)

(-) 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:212
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           DTXR_CORDI     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d2qq9a1 A:3-64 Diphtheria toxin repressor (DtxR)              d2qq9a2 A:65-139 Diphtheria toxin repressor (DtxR)                                   d2qq9a3 A:150-226 Diphtheria toxin repressor (Dtx  R)                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fe_dep_repress-2qq9A02 A:3-62                               --Fe_dep_repr_C-2qq9A01 A:65-135                                         ----          -----FeoA-2qq9A03 A:155-225                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh----------.hhhhhh....eeeeeee.hhhhh..hhhhhhhhhh.....eeeee...--..eee....eee.hhhhhhhheee.. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                PROSITE (2) -HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qq9 A   3 DLVATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG----------TRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192     | 202       212       222    
                                                                                                                                                                  139        150                                             198  |                         
                                                                                                                                                                                                                                201                         

Chain A from PDB  Type:PROTEIN  Length:212
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:224
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222    
           DTXR_CORDW     3 DLVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d2qq9a1 A:3-64 Diphtheria toxin repressor (DtxR)              d2qq9a2 A:65-139 Diphtheria toxin repressor (DtxR)                                   d2qq9a3 A:150-226 Diphtheria toxin repressor (Dtx  R)                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fe_dep_repress-2qq9A02 A:3-62                               --Fe_dep_repr_C-2qq9A01 A:65-135                                         ----          -----FeoA-2qq9A03 A:155-225                                                 - Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh----------.hhhhhh....eeeeeee.hhhhh..hhhhhhhhhh.....eeeee...--..eee....eee.hhhhhhhheee.. Sec.struct. author
             SAPs(SNPs) (1) --------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                    PROSITE -HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qq9 A   3 DLVATTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEADRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELG----------TRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDR--HITLSHNGKDVELLDDLAHTIRIEEL 226
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192     | 202       212       222    
                                                                                                                                                                  139        150                                             198  |                         
                                                                                                                                                                                                                                201                         

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QQ9)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: HTH (544)
(-)
Clan: TRB (15)

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

(-) Related Entries Specified in the PDB File

1ddn 1p92 1xcv 2qqa 2qqb 2tdx