SNAP output for PDB entry 4ut0 [SNAP web server]

PDB-id

4ut0; SNAP-derived features in text and JSON formats; DNAproDB

Class

hydrolase-DNA

Method

X-ray (2.4 Å)

Summary

The crystal structure of i-dmoi in complex with its target DNA at 10 days incubation in 5mm mn (state 7)

Reference

Molina R, Stella S, Redondo P, Gomez H, Marcaida MJ, Orozco M, Prieto J, Montoya G (2015): "Visualizing Phosphodiester-Bond Hydrolysis by an Endonuclease." Nat.Struct.Mol.Biol., 22, 65. doi: 10.1038/NSMB.2932.

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.