An enzyme lowers the activation energy through several different ways. 

1. An enzyme may position the substrates in a way that alters their bond configuration to resemble their form in the transition state. This lowers the amount of energy required to complete the transition. 
2. The enzyme may bring substrates together and position them in the correct orientation to react, thus reducing the reaction entropy. 
3. The enzyme may form new bonds in the enzyme-substrate complex, providing the reaction with a completely different chemical pathway that requires lower activation energy. 
4. The enzyme may lower the energy of the transition state by creating a charge distribution that is opposite to that of the transition state. This helps lower the activation energy.