6FWR | pdb_00006fwr

Structure of DinG in complex with ssDNA

• PDB DOI: https://doi.org/10.2210/pdb6FWR/pdb
• NAKB: 6FWR

• Classification: DNA BINDING PROTEIN
• Organism(s): Escherichia coli, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-03-07 Released: 2018-12-19 
• Deposition Author(s): Cheng, K., Wigley, D.B.
• Funding Organization(s): Medical Research Council and Cancer Research UK

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

DNA translocation mechanism of an XPD family helicase.

Cheng, K., Wigley, D.B.

(2018) Elife 7

• PubMed: 30520735 
• DOI: https://doi.org/10.7554/eLife.42400
• Primary Citation Related Structures: 
  6FWR, 6FWS


• PubMed Abstract: 
  

  The XPD family of helicases, that includes human disease-related FANCJ, DDX11 and RTEL1, are Superfamily two helicases that contain an iron-sulphur cluster domain, translocate on ssDNA in a 5'-3' direction and play important roles in genome stability. Consequently, mutations in several of these family members in eukaryotes cause human diseases. Family members in bacteria, such as the DinG helicase from Escherichia coli , are also involved in DNA repair. Here we present crystal structures of complexes of DinG bound to single-stranded DNA (ssDNA) in the presence and absence of an ATP analogue (ADP•BeF ₃ ), that suggest a mechanism for 5'-3' translocation along the ssDNA substrate. This proposed mechanism has implications for how those enzymes of the XPD family that recognise bulky DNA lesions might stall at these as the first step in initiating DNA repair. Biochemical data reveal roles for conserved residues that are mutated in human diseases.

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Organizational Affiliation: 
• Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 85.21 kDa 
• Atom Count: 5,894 
• Modeled Residue Count: 710 
• Deposited Residue Count: 727 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase DinG	A	716	Escherichia coli	Mutation(s): 0  Gene Names: dinG, CV83915_00780 EC: 5.6.2.3
UniProt
Find proteins for P27296 (Escherichia coli (strain K12)) Explore P27296  Go to UniProtKB:  P27296

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	B	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	C [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.246 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.971	α = 90
b = 133.867	β = 90
c = 58.862	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-19 
Deposition Author(s): Cheng, K., Wigley, D.B.

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Funding Organization	Location	Grant Number
Medical Research Council and Cancer Research UK	United Kingdom	MR/N009258/1

Revision History  

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references