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Biochemical and structural consequences of a glycine deletion in the α-8 helix of protoporphyrinogen oxidase

Dayan, Franck E., Daga, Pankaj R., Duke, Stephen O., Lee, Ryan M., Tranel, Patrick J., Doerksen, Robert J.
Biochimica et biophysica acta 2010 v.1804 no.7 pp. 1548
Amaranthus, Nicotiana tabacum, active sites, enzyme activity, glycine (amino acid), herbicide resistance, molecular dynamics, mutants, mutation, oxidoreductases, protein secondary structure
A rare Gly210 deletion in protoporphyrinogen oxidase (PPO) was recently discovered in herbicide-resistant Amaranthus tuberculatus. According to the published X-ray structure of Nicotiana tabacum PPO, Gly210 is adjacent to, not in, the PPO active site, so it is a matter of interest to determine why its deletion imparts resistance to herbicides. In our kinetic experiments, this deletion did not affect the affinity of protoporphyrinogen IX nor the FAD content, but decreased the catalytic efficiency of the enzyme. The suboptimal K(cat) was compensated by a significant increase in the K(i)s for inhibitors and a switch in their interactions from competitive to mixed-type inhibition. In our protein modeling studies on herbicide-susceptible PPO and resistant PPO, we show that Gly210 plays a key role in the αL helix-capping motif at the C-terminus of the α-8 helix which helps to stabilize the helix. In molecular dynamics simulations, the deletion had significant architecture consequences, destabilizing the α-8 helix-capping region and unraveling the last turn of the helix, leading to enlargement of the active site cavity by ∼ 50%. This seemingly innocuous deletion of Gly210 of the mitochondrial PPO imparts herbicide resistance to this dual-targeted protein without severely affecting its normal physiological function, which may explain why this unusual mutation was the favored evolutionary path for achieving resistance to PPO inhibitors.