4UN7

THE CRYSTAL STRUCTURE OF I-DMOI IN COMPLEX WITH ITS TARGET DNA BEFORE INCUBATION IN 5MM MN (STATE 1)

Summary for 4UN7

• Entry DOI: 10.2210/pdb4un7/pdb
• Related: 4UN6 4UN8 4UN9 4UNA 4UNB 4UNC
• Descriptor: HOMING ENDONUCLEASE I-DMOI, 25MER, ZINC ION, ... (6 entities in total)
• Functional Keywords: hydrolase-dna complex, catalysis, protein-dna interaction, hydrolase/dna
• Biological source: DESULFUROCOCCUS MOBILIS; More
• Total number of polymer chains: 9
• Total formula weight: 116094.98

Authors

Molina, R.,Stella, S.,Redondo, P.,Gomez, H.,Marcaida, M.J.,Orozco, M.,Prieto, J.,Montoya, G. (deposition date: 2014-05-26, release date: 2014-12-03, Last modification date: 2024-01-10)

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 (2.7 Å)