Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV.
Endonuclease IV belongs to a class of important apurinic/apyrimidinic endonucleases involved in DNA repair. Although a structure-based mechanistic hypothesis has been put forth for this enzyme, the detailed catalytic mechanism has remained unknown. Using thermodynamic integration in the context of ab initio quantum mechanics/molecular mechanics molecular dynamics, we examined certain aspects of the phosphodiester cleavage step in the mechanism. We found the reaction proceeded through a synchronous bimolecular (A(N)D(N)) mechanism with reaction free energy and barrier of -3.5 and 20.6 kcal/mol, in agreement with experimental estimates. In the course of the reaction the trinuclear active site of endonuclease IV underwent dramatic local conformational changes: shifts in the mode of coordination of both substrate and first-shell ligands. This qualitative finding supports the notion that structural rearrangements in the active sites of multinuclear enzymes are integral to biological function.
Ivanov
Ivaylo
I
Department of Chemistry and Biochemistry, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0365, USA. iivanov@mccammon.ucsd.edu
Tainer
John A
JA
McCammon
J Andrew
JA
D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry*; D004260:DNA Repair; D043223:Deoxyribonuclease IV (Phage T4-Induced) / Q000737:chemistry*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D007477:Ions; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011522:Protons; D013696:Temperature; D013816:Thermodynamics
D007477:Ions; D008024:Ligands; D011522:Protons; D004247:DNA; D043223:Deoxyribonuclease IV (Phage T4-Induced)