4UT0: The Crystal Structure Of I-dmoi In Complex With Its Target Dna At 10 Days Incubation In 5mm Mn (state 7)

Citation:
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.
PDB ID: 4UT0Download
MMDB ID: 125688
PDB Deposition Date: 2014/7/17
Updated in MMDB: 2014/12
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 4UT0: pentameric; determined by author and by software (PISA)
Molecular Components in 4UT0
Label Count Molecule
Protein (1 molecule)
1
Homing Endonuclease I-dmoi
Molecule annotation
Nucleotides(4 molecules)
1
5'-d(*gp*cp*cp*tp*tp*gp*cp*cp*gp*gp*gp*tp*ap*ap)-3'
Molecule annotation
1
5'-d(*cp*gp*cp*gp*cp*cp*gp*gp*ap*ap*cp*tp*tp*ap*cp)-3'
Molecule annotation
1
5'-d(*gp*tp*tp*cp*cp*gp*gp*cp*gp*cp*gp)-3'
Molecule annotation
1
5'-d(*cp*cp*gp*gp*cp*ap*ap*gp*gp*cp)-3'
Molecule annotation
Chemicals (2 molecules)
1
2
* Click molecule labels to explore molecular sequence information.

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