Wednesday, September 20, 2017 at 4:00pm to 5:00pm
Clark Hall, 700
Wei Yang, National Institute of Health
Host: Josh Chappie
Capturing transiently bound metal ions in DNA synthesis and RNA degradation reactions
Enzyme catalysis has been studied for over a century. How it actually occurs has not been visualized until recently. By combining in crystallo reaction and X-ray diffraction analysis of reaction intermediates, we have obtained unprecedented atomic details of the DNA synthesis and RNA hydrolysis process. Contrary to the established theory that enzyme-substrate complexes and transition states have identical atomic composition and catalysis occurs by the two-metal-ion mechanism, we have discovered that an additional divalent cation has to be captured en route to product formation. Unlike the canonical two metal ions, which are coordinated by enzymes, this third metal ion is free of enzyme coordination. In the DNA synthesis reaction, its location between the a- and b-phosphates of dNTP suggests that the third metal ion may drive the phosphoryltransfer from the leaving group opposite to the 3´-OH nucleophile. Experimental data indicate that binding of the third metal ion may be the rate-limiting step in DNA synthesis and the free energy associated with the metal-ion binding can overcome the activation barrier to the DNA synthesis reaction.
1. Yang, W., Weng, P.J. & Gao, Y. (2016) A new paradigm of DNA synthesis: three-metal-ion catalysis, Cell & Bioscience, online publication on Aug 2016.
2. Gao, Y. & Yang, W. (2016) Capture of a third Mg2+ is essential for catalyzing DNA synthesis, Science, 352, 1334-1337