Visualizing phosphodiester-bond hydrolysis by an endonuclease
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Visualizing phosphodiester-bond hydrolysis by an endonuclease. / Molina, Rafael; Stella, Stefano; Redondo, Pilar; Gomez, Hansel; Marcaida, María José; Orozco, Modesto; Prieto, Jesús; Montoya, Guillermo.
In: Nature Structural and Molecular Biology, Vol. 22, No. 1, 01.2015, p. 65-72.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Visualizing phosphodiester-bond hydrolysis by an endonuclease
AU - Molina, Rafael
AU - Stella, Stefano
AU - Redondo, Pilar
AU - Gomez, Hansel
AU - Marcaida, María José
AU - Orozco, Modesto
AU - Prieto, Jesús
AU - Montoya, Guillermo
PY - 2015/1
Y1 - 2015/1
N2 - 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.
AB - 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.
KW - DNA
KW - Desulfurococcaceae
KW - Endonucleases
KW - Esters
KW - Hydrolysis
KW - Models, Molecular
KW - Phosphates
KW - Protein Conformation
U2 - 10.1038/nsmb.2932
DO - 10.1038/nsmb.2932
M3 - Journal article
C2 - 25486305
VL - 22
SP - 65
EP - 72
JO - Nature Structural and Molecular Biology
JF - Nature Structural and Molecular Biology
SN - 1545-9993
IS - 1
ER -
ID: 138737420