1F5T

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

• PDB DOI:  https://doi.org/10.2210/pdb1F5T/pdb
• NAKB: 1F5T

• Classification: TRANSCRIPTION/DNA
• Organism(s): Corynebacterium diphtheriae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-06-15 Released: 2000-09-25 
• Deposition Author(s): Chen, S., White, A., Love, J., Murphy, J.R., Ringe, D.

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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 

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

• PubMed: 10956029 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.64 kDa 
• Atom Count: 5,621 
• Modelled Residue Count: 566 
• Deposited Residue Count: 570 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DIPHTHERIA TOXIN REPRESSOR	C [auth A], D [auth B], E [auth C], F [auth D]	121	Corynebacterium diphtheriae	Mutation(s): 1
UniProt
Find proteins for P0DJL7 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore P0DJL7  Go to UniProtKB:  P0DJL7

Entity ID: 1
Molecule	Chains	Length	Organism	Image
43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE	A [auth E]	43	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
43MER DNA CONTAINING DXTR CONSENSUS BINDING SEQUENCE	B [auth F]	43	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	G [auth A], H [auth A], I [auth B], J [auth B], K [auth C], L [auth C], M [auth D], N [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1F5T	Kd: 460 (nM) from 1 assay(s)

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 = 116.178	α = 90
b = 116.178	β = 90
c = 142.919	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-09-25 
Deposition Author(s): Chen, S., White, A., Love, J., Murphy, J.R., Ringe, D.

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
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations