1M0D

Crystal Structure of Bacteriophage T7 Endonuclease I with a Wild-Type Active Site and Bound Manganese Ions

Summary for 1M0D

• Entry DOI: 10.2210/pdb1m0d/pdb
• Related: 1FZR 1M0I
• Descriptor: Endodeoxyribonuclease I, MANGANESE (II) ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: holliday junction resolvase, homodimer, domain swapped, composite active site, hydrolase
• Biological source: Enterobacteria phage T7
• Total number of polymer chains: 4
• Total formula weight: 65101.72

Authors

Hadden, J.M.,Declais, A.C.,Phillips, S.E.,Lilley, D.M. (deposition date: 2002-06-12, release date: 2002-07-10, Last modification date: 2024-02-14)

Primary citation

Hadden, J.M.,Declais, A.C.,Phillips, S.E.,Lilley, D.M.
Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I.
EMBO J., 21:3505-3515, 2002

PubMed Abstract: T7 endonuclease I is a nuclease that is selective for the structure of the four-way DNA junction. The active site is similar to those of a number of restriction enzymes. We have solved the crystal structure of endonuclease I with a wild-type active site. Diffusion of manganese ions into the crystal revealed two peaks of electron density per active site, defining two metal ion-binding sites. Site 1 is fully occupied, and the manganese ion is coordinated by the carboxylate groups of Asp55 and Glu65, and the main chain carbonyl of Thr66. Site 2 is partially occupied, and the metal ion has a single protein ligand, the remaining carboxylate oxygen atom of Asp55. Isothermal titration calorimetry showed the sequential exothermic binding of two manganese ions in solution, with dissociation constants of 0.58 +/- 0.019 and 14 +/- 1.5 mM. These results are consistent with a two metal ion mechanism for the cleavage reaction, in which the hydrolytic water molecule is contained in the first coordination sphere of the site 1-bound metal ion.

PubMed: 12093751
DOI: 10.1093/emboj/cdf337

Experimental method

X-RAY DIFFRACTION (1.9 Å)