1F5T

DIPHTHERIA TOX REPRESSOR (C102D MUTANT) COMPLEXED WITH NICKEL AND DTXR CONSENSUS BINDING SEQUENCE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Methyl groups of thymine bases are important for nucleic acid recognition by DtxR.

Chen, C.S.White, A.Love, J.Murphy, J.R.Ringe, D.

(2000) Biochemistry 39: 10397-10407

  • DOI: 10.1021/bi0009284
  • Primary Citation of Related Structures:  
    1F5T

  • PubMed Abstract: 
  • The expression of diphtheria toxin is controlled by the diphtheria toxin repressor (DtxR). Under conditions of high iron concentration, DtxR binds the tox operator to inhibit transcription. To study how DNA binding specificity is achieved by this rep ...

    The expression of diphtheria toxin is controlled by the diphtheria toxin repressor (DtxR). Under conditions of high iron concentration, DtxR binds the tox operator to inhibit transcription. To study how DNA binding specificity is achieved by this repressor, we solved the crystal structure of the nickel(II) activated DtxR(C102D) mutant complexed with a 43mer DNA duplex containing the DtxR consensus binding sequence. Structural analysis of this complex and comparison with a previously determined DtxR(C102D)-Ni(II)-tox operator ternary complex revealed unusual van der Waals interactions between Ser37/Pro39 of the repressor helix-turn-helix (HTH) motif and the methyl groups of specific thymine bases in the consensus binding sequence. Gel mobility shift assays utilizing deoxyuridine modified duplex DNA probes proved the importance of these interactions: the four methyl groups shown to interact with Ser37/Pro39 in the crystal structure contribute a total of 3.4 kcal/mol to binding energy. Thus, in addition to making base-specific hydrogen-bonding interactions to the DNA through its Gln43 residue, DtxR also recognizes methyl groups at certain positions in the DNA sequence with its Ser37 and Pro39 side chains, to achieve binding specificity toward its cognate operator sequences.


    Organizational Affiliation

    Department of Biochemistry, Program in Bioorganic Chemistry, The Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454-9110, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DIPHTHERIA TOXIN REPRESSORABCD121Corynebacterium diphtheriaeMutation(s): 1 
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis))
Explore P0DJL7 
Go to UniProtKB:  P0DJL7
Protein Feature View
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  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganismImage
43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCEE43N/A
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCEF43N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download CCD File 
A, B, C, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd :  460   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.245 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.178α = 90
b = 116.178β = 90
c = 142.919γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-09-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance