Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 172.11 kDa 
• Atom Count: 11795 
• Residue Count: 1352 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2IS6

Crystal structure of UvrD-DNA-ADPMgF3 ternary complex

• DOI: 10.2210/pdb2IS6/pdb
• NDB: PD0901

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-10-16 Released: 2007-01-09 
• Deposition Author(s): Yang, W., Lee, J.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

UvrD helicase unwinds DNA one base pair at a time by a two-part power stroke.

Lee, J.Y., Yang, W.

(2006) Cell 127: 1349-1360

• PubMed: 17190599 
• DOI: 10.1016/j.cell.2006.10.049
• Primary Citation of Related Structures:  
  2IS2, 2IS1, 2IS6, 2IS4


• PubMed Abstract: 
  

Helicases use the energy derived from nucleoside triphosphate hydrolysis to unwind double helices in essentially every metabolic pathway involving nucleic acids. Earlier crystal structures have suggested that DNA helicases translocate along a single-stranded DNA in an inchworm fashion. We report here a series of crystal structures of the UvrD helicase complexed with DNA and ATP hydrolysis intermediates. These structures reveal that ATP binding alone leads to unwinding of 1 base pair by directional rotation and translation of the DNA duplex, and ADP and Pi release leads to translocation of the developing single strand. Thus DNA unwinding is achieved by a two-part power stroke in a combined wrench-and-inchworm mechanism. The rotational angle and translational distance of DNA define the unwinding step to be 1 base pair per ATP hydrolyzed. Finally, a gateway for ssDNA translocation and an alternative strand-displacement mode may explain the varying step sizes reported previously.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase II	A, B	680	Escherichia coli	Mutation(s): 1  Gene Names: uvrD EC: 3.6.1 (PDB Primary Data), 3.6.4.12 (UniProt)
Find proteins for P03018 (Escherichia coli (strain K12)) Explore P03018  Go to UniProtKB:  P03018

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*GP*AP*GP*CP*AP*CP*TP*GP*CP*AP*GP*TP*GP*CP*TP*CP*GP*TP*TP*GP*TP*TP*AP*T)-3'	C, D	25	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	A, B	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	A	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MGF	A, B	TRIFLUOROMAGNESATE F3 Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.240 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.336	α = 90
b = 96.609	β = 94.05
c = 110.93	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-10-16 
• Released Date: 2007-01-09 
Deposition Author(s): Yang, W., Lee, J.Y.

Revision History 

• Version 1.0: 2007-01-09
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description