4D6O

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA AT 1H INCUBATION IN 5MM MG (STATE 2)

Summary for 4D6O

• Entry DOI: 10.2210/pdb4d6o/pdb
• Related: 4D6N
• Descriptor: HOMING ENDONUCLEASE I-DMOI, 25MER, MAGNESIUM ION, ... (8 entities in total)
• Functional Keywords: hydrolase-dna complex, catalysis, protein-dna interaction, x-ray crystallography., hydrolase/dna
• Biological source: DESULFUROCOCCUS MOBILIS; More
• Total number of polymer chains: 9
• Total formula weight: 116087.63

Authors

Molina, R.,Stella, S.,Redondo, P.,Gomez, H.,Marcaida, M.J.,Orozco, M.,Prieto, J.,Montoya, G. (deposition date: 2014-11-13, release date: 2014-12-17, Last modification date: 2023-12-20)

Primary citation

Molina, R.,Stella, S.,Redondo, P.,Gomez, H.,Marcaida, M.J.,Orozco, M.,Prieto, J.,Montoya, G.
Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease.
Nat.Struct.Mol.Biol., 22:65-, 2015

PubMed Abstract: 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.

PubMed: 25486305
DOI: 10.1038/NSMB.2932

Experimental method

X-RAY DIFFRACTION (2.2 Å)