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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE DTXR(E175K) COMPLEXED WITH NI(II)
 
Authors :  J. A. D'Aquino, A. Denninger, A. Moulin, K. E. D'Aquino, D. Ringe
Date :  12 Mar 09  (Deposition) - 09 Jun 09  (Release) - 07 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Repressor, Regulator, Dtxr, Helix-Turn-Helix, Metal Ion, Activation, Dna-Binding, Ferrous Iron, Cytoplasm, Transcription, Transcriptional Regulation, Transcriptional Regulator, Iron, Transcription Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. D'Aquino, A. R. Denninger, A. G. Moulin, K. E. D'Aquino, D. Ringe
Decreased Sensitivity To Changes In The Concentration Of Metal Ions As The Basis For The Hyperactivity Of Dtxr(E175K).
J. Mol. Biol. V. 390 112 2009
PubMed-ID: 19433095  |  Reference-DOI: 10.1016/J.JMB.2009.05.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-11C-DTXR(E175K)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PET-11C
    Gene: DIP1414, DTXR
    Mutation: YES
    Organism Scientific: CORYNEBACTERIUM DIPHTHERIAE
    Organism Taxid: 1717
    Synonym: 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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NI-1Ligand/IonNICKEL (II) ION
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:79 , GLU A:83 , HIS A:98 , PO4 A:600BINDING SITE FOR RESIDUE NI A 551
2AC2SOFTWAREHIS A:79 , ARG A:80 , GLU A:83 , HIS A:98 , SER A:126 , PHE A:128 , ASN A:130 , HOH A:232 , HOH A:271 , NI A:551BINDING SITE FOR RESIDUE PO4 A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3GLX)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3GLX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (12, 12)

Asymmetric Unit (12, 12)
  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_007 *D199VDTXR_CORDI  ---  ---AD199V
06UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
07UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
08UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
09UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
10UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
11UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
12UniProtVAR_DTXR_CORDI_014 *I221TDTXR_CORDI  ---  ---AI221T
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (12, 24)
  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_007 *D199VDTXR_CORDI  ---  ---AD199V
06UniProtVAR_DTXR_CORDI_008 *H201RDTXR_CORDI  ---  ---AH201R
07UniProtVAR_DTXR_CORDI_009 *S205RDTXR_CORDI  ---  ---AS205R
08UniProtVAR_DTXR_CORDI_010 *I214LDTXR_CORDI  ---  ---AL214L
09UniProtVAR_DTXR_CORDI_011 *I214YDTXR_CORDI  ---  ---AL214Y
10UniProtVAR_DTXR_CORDI_012 *A218TDTXR_CORDI  ---  ---AA218T
11UniProtVAR_DTXR_CORDI_013 *I221MDTXR_CORDI  ---  ---AI221M
12UniProtVAR_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 3GLX)

(-) Exons   (0, 0)

(no "Exon" information available for 3GLX)

(-) 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:211
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225 
           DTXR_CORDI     6 DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIEEL 226
               SCOP domains d3glxa1 A:6-64 automated matches                           d3glxa2 A:65-140 automated matches                                                 d3glxa3 A:148-226 automated matches                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.-------..eehhhhh....eeeeeee.hhhhh...hhhhhhhhh..............-..eee.--..ee.hhhhhhhheee.. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T-------V-R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glx A   6 DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVKTDQFTQLLDADIRVGSEVEIVDRD-HITLSH--KDVELLDDLAHTIRIEEL 226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135    |    -  |    155       165       175       185       195   | | 205|  |   215       225 
                                                                                                                                                                140     148                                                199 |  206  |                 
                                                                                                                                                                                                                             201     209                 


Chain A from PDB  Type:PROTEIN  Length:211
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225 
           DTXR_CORDW     6 DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIEEL 226
               SCOP domains d3glxa1 A:6-64 automated matches                           d3glxa2 A:65-140 automated matches                                                 d3glxa3 A:148-226 automated matches                                             SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.-------..eehhhhh....eeeeeee.hhhhh...hhhhhhhhh..............-..eee.--..ee.hhhhhhhheee.. Sec.struct. author
             SAPs(SNPs) (1) -----------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T-------V-R---R--------L---T--M----- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T----- SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3glx A   6 DTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVKTDQFTQLLDADIRVGSEVEIVDRD-HITLSH--KDVELLDDLAHTIRIEEL 226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135    |    -  |    155       165       175       185       195   | | 205|  |   215       225 
                                                                                                                                                                140     148                                                199 |  206  |                 
                                                                                                                                                                                                                             201     209
   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
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3GLX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3GLX)

(-) Gene Ontology  (7, 14)

Asymmetric Unit(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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  DTXR_CORDW | H2I233
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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 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx
        DTXR_CORDW | H2I233: 1bi0 1bi1 1bi2 1bi3 1bym 1c0w 1ddn 1dpr 1f5t 1fwz 1g3s 1g3t 1g3w 1g3y 1p92 1qvp 1qw1 1xcv 2dtr 2qq9 2qqa 2qqb 2tdx

(-) Related Entries Specified in the PDB File

1ddn 1p92 1xcv 2qq9 2qqa 2qqb