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research article

Visualizing phosphodiester-bond hydrolysis by an endonuclease

Molina, Rafael
•
Stella, Stefano
•
Redondo, Pilar
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2014
Nature structural & molecular biology

The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.

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Type
research article
DOI
10.1038/nsmb.2932
Author(s)
Molina, Rafael
Stella, Stefano
Redondo, Pilar
Gomez, Hansel
Marcaida, María José
Orozco, Modesto
Prieto, Jesús
Montoya, Guillermo
Date Issued

2014

Published in
Nature structural & molecular biology
Volume

22

Issue

1

Start page

65

End page

72

Editorial or Peer reviewed

NON-REVIEWED

Written at

EPFL

EPFL units
IBI-SV  
Available on Infoscience
November 9, 2016
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/130993
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